Other bits:
I've seen in the capture i threw into sekaiju that the MT-32 has more tracks than the General midi for the few games i've been experimenting with.
Sometimes, MT-32 'instruments' can be sound effects or complex sounds that General MIDI cannot emulate, therefore the MIDI track gets deleted. I'm not familiar with this game. I would imagine it is not common but does happen. In such a case, the MT-32 track can be added back to the GM track, if you feel it can be converted to a GM instrument, but was not done for whatever reason by the original sound team.
I'm fine with the idea of recording hte "entire session" and just quickly skipping to save points where i know the music will play, the point was to trip dead air around it.
I would encourage you to start and stop recording for each individual music track, because it's much easier to edit MIDI data that way. That is to say, removing extra bits at the start and then ending the file the way you want, either with a finish or with a fade out. The complexity of working with MIDI exponentially increases with the length of the file. You will not want to have an hour's capture where you have to fiddle in and out of insanely detailed MIDI channels of note and controler events, split them up, and so on.
So in theory there is a risk though that the trakcs may change the sysex compared to the start of game and i really just never know?
With MT-32 output, yes, not with GM. Typically this does not happen for instruments themselves, and if that did happen, you would know because the track would sound weird. Reverb is much harder to tell after the fact.
and dosbox's midi capture doesnt' actually keep a record of the sysex if in mt32 output mode and apply it to any capture, i have to capture at the start of teh session?
SysEx is a MIDI event, so yes, DOSBox captures it.. but it will not 'apply' it, it will just have the raw data present at the start of your recording. What you should do is record the SysEx once and remove any song data from it, then play it back to the MT-32/MUNT before beginning doing any editing work in a session. This will ensure you have initialised the MT-32 with the SysEx correctly. The initial SysEx when a game opens is the most important dataset that the MT-32 is loaded with.
I'll probably end up going to GM eventually, but mt32's one of those, "i have to know" type things, if htat makes sense.
See my previous post. This is a many-years-long thing to understand, not a quick nerdy deep dive. There's nothing wrong with wanting to learn and I think it's cool you are trying, but you will need a much larger level of understanding before you are able to do even MT-32 MIDI the way you want, let alone converting that data to something else. If your true aim is rerecording old game music with new soundfonts, then the MT-32 data should be avoided at this time.