I think all of the info in here is correct, just to add in:
- Kotobuki mugens were made without JKA seals, as Iwata was having disagreements with the JKA. They were the last JKA-shaped mugens made. (red with gold speckles, blue with gold speckles)
- Some of the rare colours were produced as gifts for contest attendees (sparkly purple, poke ball, etc), so they would just be confined to whichever generation was being made at that time. i.e. there are not poke ball mugen 1s, and poke ball mugen 2s. It would be one or the other.
- I know Tamotsu also liked having a hole drilled in base cup, I thought that part of the musou design was from his input. I've met Ito-san as well, I don't recall him having bottom cup holes specifically, but I might have just missed that. I received my first mugen from him!