It's fairly easy to distinguish project outputs and pretty hard to do it for inputs.
And it's quite impossible to, in example, allow different fuels for the same project. So any realistic suggestion can touch only the game interface.
Instead of current dropdown list with more-or-less random order I suggest to create list with radio buttons grouped by output material. Best would be something like ajax build menu, but I don't know how to do it. Simple static list would still be better than current interface.
How it could look like:
![Image](http://cantr-mmorpg.pl/cantr-features/gui-machine-projs.jpeg)