Have you tried changing:
else if (!this.mergeItemStack(var5, 2, 3, false))
{
return null;
}
to:
else if (!this.mergeItemStack(var5, 3, 4, false))
{
return null;
}
I am only just touching on creating a new furnace myself but from what I can tell your new input slot is 3 so I imagine that it would look like that. But I'm just guessing.