God you're piling yourself a mountain of complexity. An entire book here...
First of all, the file MoM saves it's settings into is config.mom. Install.exe doesn't corrupt anything, something's wrong - run it again, re-configure and save again.
Second, if you set an incorrect IRQ or DMA the game does crash because of hardware conflict with the soundcard settings. Nothing to worry about there, boot up the system again.
Third, the game shouldn't care at all where you install it since it's a Dos game and doesn't require a CD when installed and running, so juggling with the partitions isn't necessary. It does help though if you run it on earlier Dos version than 7.1 since this one is less compatible with the earlier ones. Particularly 6.22 is the best for any Dos games, earlier again like 6.0 and 5.0 are worse due to lack of good programs and older, less efficient versions of memory managers to load.
Another thing is that without Dos drivers for the soundcard to load and stay in memory most games don't recognize any Soundblaster, so you have to load those up at booting. Why I proposed IRQ 5 and DMA 1 instead of the ones you use is because both settings (the ones you use and ones I proposed) are standards for Soundblaster settings in Dos, so if one setting doesn't work, try the other one.
Having Windows 98 being actively used and a disagreeable BIOS that isn't very configurable also causes often lots of troubles between Dos, soundcard settings and games which don't find any normal settings to use. A clean Dos system is much better for Dos games than Windows 98 unless one has a very good knowledge about old systems and how to work on all of their hardware / software settings. That said, the system you mention doesn't seem to be very optimal for Dos games but heavy-aligned towards Windows 98 instead.
The game does use MIDI music so choose Soundblaster MIDI (OPL2 / OPL3) for music. The installer usually automatically sets the default adress for MIDI which should usually work, too, since it changes only in rare cases.
About which Soundblaster to choose, the models of Soundblaster cards from earliest (worst) to latest (best) in ascending order - Soundblaster, Soundblaster 2.0 (few games only differenate between the two), Soundblaster PRO (earlier), Soundblaster PRO (later, with Stereo), Soundblaster 16. Those are the Soundblaster standards used in Dos games, so obviously choosing Soundblaster 16 is the best option if you have that or a later Soundblaster card.
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