The problem was all the digital samples were not convertible into something more contemporary. The .snd file for the squeaker speaker appeared to be raw PWM data. The Adlib used assembly to hand-make the sound effects, and the Sound-blaster VOC files have their own special problems. It seems that even though back in the day VOCs were ubiquitous, they were also proprietary. Creative labs never released the actual format. There are a few programs that can read VOC files, but the ones I have are packed and not readable, or covertable by any of my legacy software.
This is not a especially terrible thing. The samples are rips from the original 60's Star Trek and need to be replaced anyway. I know where each effect is played in the game so I can hunt some sounds that are more appropriate for the game.
The last pass I have is allowing me to fix up Nermal once and foe all, and support high resolutions. One of my core functions, the blitter, is super hacky and I now have an opportunity to fix that, and most of the other functions, once and for all.
The credits roll in glorious 1280x800 now :)