Michael,

Please don't spend any time on my behalf resolving these details. It was just something I was playing around with.

I ended up taking the previous .obj import (from Max's script as I mentioned earlier), and exported as STEP then placed into Onshape and performed what fillets I could there. Then imported back into MoI and added the kitbash items there, along with a calculated fillet (the one where you sweep a circle along a path, bool diff it from the model and stitch it back up with Blend and Network).

The places you point to are obvious errors introduced in Onshape or when exported as STEP from Onshape.

Good to know. Thanks for your help. :-)