For your MIDI files, you can try using OpenMP. Just open your file, then fix instruments if needed, and export it as IT file, with instruments integration.
Hope it will help.
For SPC files, i don't know of another solution other than the one you used, sorry.
Edit : After some thoughts, you can do it with SPC files too : once you have your converted IT files, you can modify them in OpenMPT and fix sustained keypresses.