I figured that the order of complexity is ore -> intermediate (ranging from complexity) -> finished item -> last step?
I might be wrong, but it seemed like that. I don't think you need to order them since, a factory module (say inserter), next to an upgrade most often than not lines up for the last item to be made. (hope that made sense xD) But you could probably have it as a mod setting to let players do whatever order. just an idea.
And i had another idea, but it involved having your own entities, like in Bob's mod, there are certain assemblers for electronics, 2x2 ones, and normal assemblers 3x3, and what not. Why not something like a smaller assembler for your mod? Again, it's just an idea, and might be something you might wanna do. :P
Again, pretty fun, and pretty hectic when red circuits come in. ;')