[1.7.2] Custom Furnace Troubles

I have been doing a bit of experimenting with some mod creation and a custom furnace.  My problem is that when I put something into the smelting slot [Slot 0] it just moves over to the fuel slot [Slot 1] and replaces the item already there. Any help would be wonderful. Thanks.

ContainerGingaFurnace.java

package net.gingacraft.mod.container;

import cpw.mods.fml.relauncher.Side;
import cpw.mods.fml.relauncher.SideOnly;
import net.gingacraft.mod.Gingacraft;
import net.gingacraft.mod.tileentity.TileEntityGingaFurnace;
import net.minecraft.client.resources.I18n;
import net.minecraft.entity.player.EntityPlayer;
import net.minecraft.entity.player.InventoryPlayer;
import net.minecraft.inventory.Container;
import net.minecraft.inventory.ICrafting;
import net.minecraft.inventory.Slot;
import net.minecraft.inventory.SlotFurnace;
import net.minecraft.item.ItemStack;
import net.minecraft.item.crafting.FurnaceRecipes;
import net.minecraft.tileentity.TileEntityFurnace;
import net.minecraft.util.ResourceLocation;

public class ContainerGingaFurnace extends Container{
	
	private TileEntityGingaFurnace gingaFurnace;
	
	public int lastBurnTime;
	public int lastCurrentItemBurnTime;
	public int lastCookTime;
	
	public ContainerGingaFurnace(InventoryPlayer inventory, TileEntityGingaFurnace tileentity){
		this.gingaFurnace = tileentity;
		
		this.addSlotToContainer(new Slot(tileentity, 0, 56, 35));
		this.addSlotToContainer(new Slot(tileentity, 1, 8, 62));
		this.addSlotToContainer(new SlotFurnace(inventory.player, tileentity, 2, 116, 35));
		
		for(int i = 0; i < 3; i++){
			for(int j = 0; j < 9; j++){
				this.addSlotToContainer(new Slot(inventory, j + i * 9 + 9, 8 + j * 18, 84 + i * 18));
			}
		}
		for(int i = 0; i < 9; i++){
			this.addSlotToContainer(new Slot(inventory, i, 8 + i * 18, 142));
		}	
	}
	
	public void addCraftingToCrafters (ICrafting icrafting){
		super.addCraftingToCrafters(icrafting);
		icrafting.sendProgressBarUpdate(this, 0, this.gingaFurnace.cookTime);
		icrafting.sendProgressBarUpdate(this, 1, this.gingaFurnace.burnTime);
		icrafting.sendProgressBarUpdate(this, 2, this.gingaFurnace.currentItemBurnTime);
	}
	
	public void detectAndSendChanges(){
		super.detectAndSendChanges();
		for(int i = 0; i < this.crafters.size(); i++){
			ICrafting icrafting = (ICrafting) this.crafters.get(i);
			
			if(this.lastCookTime != this.gingaFurnace.cookTime){
				icrafting.sendProgressBarUpdate(this, 0, this.gingaFurnace.cookTime);
			}
			if(this.lastBurnTime != this.gingaFurnace.burnTime){
				icrafting.sendProgressBarUpdate(this, 1, this.gingaFurnace.burnTime);
			}
			if(this.lastCurrentItemBurnTime != this.gingaFurnace.currentItemBurnTime){
				icrafting.sendProgressBarUpdate(this, 2, this.gingaFurnace.currentItemBurnTime);
			}	
		}
		this.lastCookTime = this.gingaFurnace.cookTime;
		this.lastBurnTime = this.gingaFurnace.burnTime;
		this.lastCurrentItemBurnTime = this.gingaFurnace.currentItemBurnTime;
	}
	
	@SideOnly(Side.CLIENT)
	public void updateProgressBar(int slot, int par2){
		if (slot == 0){
			this.gingaFurnace.cookTime = par2;
		}
		if (slot == 1){
			this.gingaFurnace.burnTime = par2;
		}
		if (slot == 2){
			this.gingaFurnace.currentItemBurnTime = par2;
		}
	}
	
    public ItemStack transferStackInSlot(EntityPlayer par1EntityPlayer, int par2){
        ItemStack itemstack = null;
        Slot slot = (Slot)this.inventorySlots.get(par2);

        if (slot != null && slot.getHasStack()){
            ItemStack itemstack1 = slot.getStack();
            itemstack = itemstack1.copy();

            if (par2 == 2){
                if (!this.mergeItemStack(itemstack1, 3, 39, true)){
                    return null;
                }

                slot.onSlotChange(itemstack1, itemstack);
            }
            else if (par2 != 1 && par2 != 0){
                if (FurnaceRecipes.smelting().getSmeltingResult(itemstack1) != null){
                    if (!this.mergeItemStack(itemstack1, 0, 1, false)){
                        return null;
                    }
                }
                else if (TileEntityGingaFurnace.isItemFuel(itemstack1)){
                    if (!this.mergeItemStack(itemstack1, 1, 2, false)){
                        return null;
                    }
                }
                else if (par2 >= 3 && par2 < 30){
                    if (!this.mergeItemStack(itemstack1, 30, 39, false)){
                        return null;
                    }
                }
                else if (par2 >= 30 && par2 < 39 && !this.mergeItemStack(itemstack1, 3, 30, false)){
                    return null;
                }
            }
            else if (!this.mergeItemStack(itemstack1, 3, 39, false)){
                return null;
            }

            if (itemstack1.stackSize == 0){
                slot.putStack((ItemStack)null);
            }
            else{
                slot.onSlotChanged();
            }

            if (itemstack1.stackSize == itemstack.stackSize){
                return null;
            }

            slot.onPickupFromSlot(par1EntityPlayer, itemstack1);
        }

        return itemstack;
    }
	@Override
	public boolean canInteractWith(EntityPlayer var1) {
		return true;
	}
}

TileEntityGingaFurnace.java

package net.gingacraft.mod.tileentity;

import cpw.mods.fml.common.registry.GameRegistry;
import net.gingacraft.mod.Gingacraft;
import net.gingacraft.mod.blocks.GingaFurnace;
import net.minecraft.block.Block;
import net.minecraft.entity.player.EntityPlayer;
import net.minecraft.init.Blocks;
import net.minecraft.init.Items;
import net.minecraft.inventory.ISidedInventory;
import net.minecraft.item.ItemBlock;
import net.minecraft.item.ItemStack;
import net.minecraft.item.crafting.FurnaceRecipes;
import net.minecraft.nbt.NBTTagCompound;
import net.minecraft.nbt.NBTTagList;
import net.minecraft.tileentity.TileEntity;
import net.minecraft.util.WeightedRandom.Item;

public class TileEntityGingaFurnace extends TileEntity implements ISidedInventory{
	
	private String localizedName;
	
	private static final int[] slots_top = new int[]{0};
	private static final int[] slots_bottom = new int[]{2, 1};
	private static final int[] slots_side = new int[]{1};
	
	private ItemStack[] slots = new ItemStack [3];
	
	public int furnaceSpeed = 150;
	public int burnTime;
	public int currentItemBurnTime;
	public int cookTime;
	
	public void setGuiDisplayName(String displayName){
		this.localizedName = displayName;
	}

	public String getInventoryName(){
		return this.hasCustomInventoryName() ? this.localizedName : "container.gingaFurnace";
	}

	public boolean hasCustomInventoryName() {
		return this.localizedName != null && this.localizedName.length() > 0;
	}
	
	public int getSizeInventory(){
		return this.slots.length;
	}

	@Override
	public ItemStack getStackInSlot(int var1) {
		return this.slots[var1];
	}

	@Override
	public ItemStack decrStackSize(int var1, int var2){
		if(this.slots[var1] != null){
			ItemStack itemstack;
			
			if(this.slots[var1].stackSize <= var2 ){
				itemstack = this.slots[var1];
				this.slots[var1] = null;
				return itemstack;
			}else{
				itemstack = this.slots[var1].splitStack(var2);
				
				if(this.slots[var1].stackSize == 0){
					this.slots[var1] = null;
				}
				
				return itemstack;
			}
		}
		else{
			return null;
		}
	}

	@Override
	public ItemStack getStackInSlotOnClosing(int i){
		if(this.slots[i] != null){
			ItemStack itemstack = this.slots[i];
			this.slots[i] = null;
			return itemstack;
		}
		return null;
	}

	@Override
	public void setInventorySlotContents(int i, ItemStack itemstack){
		this.slots[1] = itemstack;
		
		if(itemstack != null && itemstack.stackSize > this.getInventoryStackLimit()){
			itemstack.stackSize = this.getInventoryStackLimit();
		}
	}

	@Override
	public int getInventoryStackLimit(){
		return 64;
	}

	@Override
	public boolean isUseableByPlayer(EntityPlayer entityplayer){
		return this.worldObj.getTileEntity(this.xCoord, this.yCoord, this.zCoord) != this ? false : entityplayer.getDistanceSq((double)this.xCoord + 0.5D, (double)this.yCoord + 0.5D, (double)this.zCoord + 0.5D) <= 64.0D;
	}

	
	public void openInventory() {}
	public void closeInventory() {}

	@Override
	public boolean isItemValidForSlot(int i, ItemStack itemstack){
		return i == 2 ? false : (i == 1 ? isItemFuel(itemstack) : true);
	}
	
	public static boolean isItemFuel (ItemStack itemstack){
		return getItemBurnTime(itemstack) > 0;
	}

	private static int getItemBurnTime(ItemStack itemstack){
		if(itemstack == null){
			return 0;
		}else{ //net.minecraft.item.Item
			net.minecraft.item.Item item = itemstack.getItem();
			
			if(item instanceof ItemBlock && Block.getBlockFromItem(item) != Blocks.air){
				Block block = Block.getBlockFromItem(item);
				
				if(block == Blocks.sapling) return 100;
				if(block == Blocks.coal_block) return 14400;
			}	
			
			if(item == Gingacraft.itemTreePitch) return 800;
			if(item == Items.coal) return 1600;
			if(item == Items.stick) return 100;
			if(item == Items.lava_bucket) return 20000;
			if(item == Items.blaze_rod) return 2400;
		}
		
		return GameRegistry.getFuelValue(itemstack);
	}
	
	public boolean isBurning(){
		return this.burnTime > 0;
	}
	
	public void updateEntity(){
		boolean flag = this.burnTime > 0;
		boolean flag1 = false;
		
		if(this.isBurning()){
			this.burnTime--;
		}
		if(!this.worldObj.isRemote){
			if(this.burnTime == 0 && this.canSmelt()){
				this.currentItemBurnTime = this.burnTime = getItemBurnTime(this.slots[1]);
				
				if(this.isBurning()){
					flag1 = true;
					
					if(this.slots[1] != null){
						this.slots[1].stackSize--;
						
						if(this.slots[1].stackSize == 0){
							this.slots[1] = this.slots[1].getItem().getContainerItem(this.slots[1]);
						}
					}
				}
			}
			if(this.isBurning() && this.canSmelt()){
				this.cookTime++;
				
			if(this.cookTime == this.furnaceSpeed){
				this.cookTime = 0;
				this.smeltItem();
				flag1 = true;
			}
			}else{
				this.cookTime = 0;
			}
			
			if(flag != this.isBurning()){
				flag1 = true;
				GingaFurnace.updateGingaFurnaceBlockState(this.burnTime > 0, this.worldObj, this.xCoord, this.yCoord, this.zCoord);
			
			}
		}
		if(flag1){
			this.markDirty();
		}
	}
	
	public boolean canSmelt(){
		if(this.slots[0] == null){
			return false;
		}else{
			ItemStack itemstack = FurnaceRecipes.smelting().getSmeltingResult(this.slots[0]);
			
			if(itemstack == null) return false;
			if(this.slots[2] == null) return true;
			if(this.slots[2].isItemEqual(itemstack)) return false;
			
			int result = this.slots[2].stackSize + itemstack.stackSize;
			
			return (result <= getInventoryStackLimit() && result <= itemstack.getMaxStackSize());
		}
	}		
			
	public void smeltItem(){
		if(this.canSmelt()){
			ItemStack itemstack = FurnaceRecipes.smelting().getSmeltingResult(this.slots[0]);
			
			if(this.slots[2] == null) {
				this.slots[2] = itemstack.copy();
			}else if (this.slots[2].isItemEqual(itemstack)){
				this.slots[2].stackSize += itemstack.stackSize;
			}
			
			this.slots[0].stackSize--;
			
			if(this.slots[0].stackSize <= 0){
				this.slots[0] = null;
			}
		}
	}			
		
	@Override
	public int[] getAccessibleSlotsFromSide(int var1) {
		return var1 == 0 ? slots_bottom : (var1 == 1 ? slots_top : slots_side);
	}

	@Override
	public boolean canInsertItem(int i, ItemStack itemStack, int j) {
		return this.isItemValidForSlot(i, itemStack);
	}

	@Override
	public boolean canExtractItem(int i, ItemStack itemStack, int j) {
		return j != 0 || i != 1 || itemStack.getItem() == Items.bucket;
	}
	
	public int getBurnTimeRemainingScaled(int i){
		if(this.currentItemBurnTime == 0){
			this.currentItemBurnTime = this.furnaceSpeed;
		}
		return this.burnTime * i / this.currentItemBurnTime;
	}
	public int getCookProgressScaled(int i){
		return this.cookTime * i / this.furnaceSpeed;
	}
	public void readFromNBT(NBTTagCompound nbt) {
		super.readFromNBT(nbt);
		
		NBTTagList list = nbt.getTagList("Items", 10);
		this.slots = new ItemStack[this.getSizeInventory()];
		
		for(int i = 0; i < list.tagCount(); i++) {
			NBTTagCompound compound = (NBTTagCompound) list.getCompoundTagAt(i);
			byte b = compound.getByte("Slot");
			
			if(b >= 0 && b < this.slots.length) {
				this.slots[b] = ItemStack.loadItemStackFromNBT(compound);
			}
		}
		
		this.burnTime = (int)nbt.getShort("BurnTime");
		this.cookTime = (int)nbt.getShort("CookTime");
		this.currentItemBurnTime = (int)nbt.getShort("CurrentBurnTime");
		
		if(nbt.hasKey("CustomName")) {
			this.localizedName = nbt.getString("CustomName");
		}
	}
	
	public void writeToNBT(NBTTagCompound nbt) {
		super.writeToNBT(nbt);
		
		nbt.setShort("BurnTime", (short)this.burnTime);
		nbt.setShort("CookTime", (short)this.cookTime);
		nbt.setShort("CurrentBurnTime", (short)this.currentItemBurnTime);
		
		NBTTagList list = new NBTTagList();
		
		for (int i = 0; i < this.slots.length; i++) {
			if(this.slots[i] != null) {
				NBTTagCompound compound = new NBTTagCompound();
				compound.setByte("Slot", (byte)i);
				this.slots[i].writeToNBT(compound);
				list.appendTag(compound);
			}
		}
		
		nbt.setTag("Items", list);
		
		if (this.hasCustomInventoryName()) {
			nbt.setString("CustomName", this.localizedName);
		}
	}
}

GuiGingaFurnace.java

package net.gingacraft.mod.gui;

import org.lwjgl.opengl.GL11;

import net.gingacraft.mod.Gingacraft;
import net.gingacraft.mod.container.ContainerGingaFurnace;
import net.gingacraft.mod.tileentity.TileEntityGingaFurnace;
import net.minecraft.client.Minecraft;
import net.minecraft.client.gui.inventory.GuiContainer;
import net.minecraft.client.resources.I18n;
import net.minecraft.entity.player.InventoryPlayer;
import net.minecraft.inventory.Container;
import net.minecraft.tileentity.TileEntityFurnace;
import net.minecraft.util.ResourceLocation;

public class GuiGingaFurnace extends GuiContainer{

	public static final ResourceLocation bground = new ResourceLocation(Gingacraft.modid + ":" + "textures/gui/GuiGingaFurnace.png");

	public TileEntityGingaFurnace gingaFurnace;
	
	public GuiGingaFurnace(InventoryPlayer inventoryPlayer, TileEntityGingaFurnace entity) {
		super(new ContainerGingaFurnace(inventoryPlayer, entity));
			
		this.gingaFurnace = entity;
			
		this.xSize = 176;
		this.ySize = 166;
		}
		
	public void drawGuiContainerForegroundLayer(int par1, int par2){
		String name = this.gingaFurnace.hasCustomInventoryName() ? this.gingaFurnace.getInventoryName() : I18n.format(this.gingaFurnace.getInventoryName(), new Object[0]);
		this.fontRendererObj.drawString(name, this.xSize / 2 - this.fontRendererObj.getStringWidth(name) / 2, 10, 16093987);
		this.fontRendererObj.drawString(I18n.format("container.inventory", new Object[0]), 118, this.ySize - 96 + 2, 16093987);
	}
	
	@Override
	protected void drawGuiContainerBackgroundLayer(float var1, int var2, int var3) {
		GL11.glColor4f(1F, 1F, 1F, 1F);
		
		Minecraft.getMinecraft().getTextureManager().bindTexture(bground);
		drawTexturedModalRect(guiLeft, guiTop, 0, 0, xSize, ySize);
		
		if(this.gingaFurnace.isBurning()){
			int k = this.gingaFurnace.getBurnTimeRemainingScaled(40);
			int j = 40 - k;
			drawTexturedModalRect(guiLeft + 29, guiTop + 65, 176, 0, 40 - j, 10);
		}
		int k = this.gingaFurnace.getCookProgressScaled(24);
		drawTexturedModalRect(guiLeft + 79, guiTop + 34, 176, 10, k + 1, 16);
		
	}
}

GingaFurnace.java

package net.gingacraft.mod.blocks;

import cpw.mods.fml.relauncher.Side;
import cpw.mods.fml.relauncher.SideOnly;
import net.gingacraft.mod.Gingacraft;
import net.minecraft.block.Block;
import net.minecraft.block.material.Material;
import net.minecraft.client.renderer.texture.IIconRegister;

public class GingaBlock extends Block {
	
	public GingaBlock(Material material){
		super(material);
		
		this.setStepSound(soundTypeMetal);
		this.setCreativeTab(Gingacraft.gingacraftTab);
	}
	
	@SideOnly(Side.CLIENT)
	public void registerBlockIcons(IIconRegister iconRegister) {
		this.blockIcon = iconRegister.registerIcon(Gingacraft.modid + ":" + this.getUnlocalizedName().substring(5));
	}
}