A little update: I got in contact with natt and zeromus of Bizhawk. We chatted and looks like the emulator will get an update with the new requested features.
I should be able to convert the rom back into source code with these features. It gives me the CDL file, and a trace log format that gives the SF2 bank #, regular bank #, and logical address along with the opcode bytes.
With this, and a playthrough of a game - I can rebuild the binary back into source code. I plan to do this for SF2 and Bonk. This is pretty awesome!