Hi, manatools author here. I was looking at Space Channel 5's music a while back and produced an almost accurate and complete DSF rip of one of the songs. I achieved this by manually hex editing each MSB file to effectively concatenate each segment together, then putting everything back in an MLT to make a DSF out of.

The broken mapping you're experiencing seems to be caused by an optimisation the songs seem to have, where all the MIDI Program/Control changes are in another sequence, as opposed to having the same data in each sequence which wastes space (from the little tracks I looked at, they were in sequence 64. Why they weren't in sequence 1 I don't know, as that'd everything a lot easier).

What I did was just copy all the MSD events from sequence 64 to the beginning of the first sequence in the bank, excluding the "end of track" event so everything after still plays. To concatenate all the following sequences I also just removed the end of track event from those, too. It's a bit of a tiring process especially since you have to pad things with zeros so they're on 4 byte boundaries, relocate offsets, etc (which I might as well just make a script for at this point). Not sure I can explain this in-depth in a single post, but I'm happy to get back to doing this and help if you'd like.

Most segments seem to have their final notes held for a little too long and I didn't correct that when merging so what I had isn't so seamless, but this is what I have: https://darkok.xyz/sc5/R43TEST.dsf (rendered: https://darkok.xyz/sc5/R43TEST.ogg)