About the MSU-1 compatibility:
A way to start, would be to have 3 ROMs ready.
1) Vanilla MK
2) Proper MSU-1 MK
3) Champion+Uncensored MK
The method to start debugging this from my perspective, would be to compare the vanilla MK ROM against the MSU-1 patched ROM with a Hex comparison.
Once the start of the MSU-1 code is located, we need to take the address and code from the vanilla ROM where the MSU-1 code would start, and then try to find the matching section of code from the vanilla ROM into the Champion ROM.
Once that's located, then that'd be the new place to start the hijack in the Champion ROM for the MSU-1 hack. This would need to be done for every hijack the MSU-1 does, and move the hijack's JSR/JMP to free space of the Champion ROM to make it fully compatible.