You misunderstand... not to be printed separately, but printed in different colors at the same time. The MMU2 and Palette are products that enable a single extruder printer to print in up to 4 (Palette) or 5 (MMU2) colors. Same print. No assembling needed. I assumed you were aware of this. My bad. I have an MMU2, and would love to print this in multiple colors. I have Fusion 360. It says it can open Inventor files.
Editing STL files is a pain. The original files would be much easier to work with. It's up to you, if you want to send them to me. If you understand what I mean now, maybe you'll have a different answer. You need NOT change your model in any way, other than to split a few parts into a couple pieces so that they can be individually assigned different colors on a multi-color printer.