The problem I'm running into is the need to constantly switch out physical upgrade modules to achieve the performance I'd like to see.

For example, sometimes I'm on cleanup/deconstruct detail, so I swap all the modules out for deconstructs and cleanups. Then, next I'd like to build a projected ship, so I have to switch them all out for projectors/constructions.

As a suggestion, what about making the purpose of the nanite configurable in the control panel for the factory, and then have the upgrade modules simply be generic modules that increase the total number of nanites to devote to various tasks?

So, for example, the base factory maybe has 4 nanites (defaulted to one to each task). However, using sliders (or something within the contorl panel) you could devote more of a percentage of nanites to any particular task. So, if you slid the "cleanup" bar all the way to the right, all 4 of the nanites would be on cleanup detail.

Then, adding an upgrade module would simply increase the total number of available nanites by an additional 3 or 4 or whatever.

Just a suggestion; I believe it would simplify the process and make the system more flexible while still being large and power hungry to balance it.