See http://mod-buildcraft.com/forums/index.php?topic=719.0

It's potentially a two fold solution to be looked at:

• replace one block type by another
• allow a given slot to be filled by whatever block available in a given category (e.g., expect wood planks, take whichever wood planks)

Note: Not closing this yet as it depends on the single schematic item being finished to be usable (even though it has been completely implemented)

Why not making a way to make some blocks in a blueprint shapless. And the Builder has a slot/Slots for shapeless blocks. That could be a way. So you do not need to change the blocks always for every little things.

I didn't know this existed. I'm having some trouble with gui on this.
http://mod-buildcraft.com/forums/index.php?topic=743.0
I don't know what the problem could be at this point.