This is my attempt at sending a packet to do it:
Packet102WindowClick wc = new Packet102WindowClick();
wc.window_Id = 2; // Furnace
wc.inventorySlot = 2; // Output
wc.mouseClick = 0; // Left click
wc.holdingShift = true; // Get it all
wc.action = minecraft.thePlayer.craftingInventory.getNextTransactionID(minecraft.thePlayer.inventory);
wc.itemStack = finishedStack;
ModLoader.sendPacket(wc);
logger.info("Transferred!");
EDIT: This works!!!!! :D:D:D:D