(one guy's experience with FF1 engine)
1..Several mega man 2 3 and 4 rom hacks use lots of new music, but they were done with assembly. It looks like they disassembled the (level hacked and graphics hacked) original rom, and replaced the sound engine with famitone. https://github.com/nesdoug/famitone4.1
2..You CAN reassemble it with the original sound engine, but you then have to figure out its music format and how to assemble the songs.
3..The other way to do this (which i do not recommend) is by figuring out the music format by identifying music playing in the memory viewer, tracing its values back to the rom, and finally hex editing the notes or the timing.
It helps to have famitracker save as txt for this.
I am still trying to wrap my head around the process myself, since I've been playing around with Zelda II lately. I have similar goals for a Zelda 2 project but I'm no ASM expert, so I'm still trying to figure out how to reassemble this mess XD
I used smartrenes for disassembly, I'm planning on using cc65 to reassemble. Maybe someone can offer some more experienced insight on the nature of hacking the sound processor.
There IS a capcom music editor but it likes to crash, it's missing features etc. http://www.romhacking.net/utilities/1245/
I think it only works for megaman 3 4 5 and 6.