Hello! Nice project you've got here 😀 , so trying to bring my two cents:
Teamster is right (good ear for a non-musician btw 😉 ), in the SQ3 MP3 on the site, the first theme (syn brass?) is played one major third down, so playing A4 instead of C5 for instance. It sounds more accurate in the version currently available but that's not it yet. It's difficult to say for that theme as in the current version, the volume of that track is too low, and definitely lower than in the site's MP3. I made some tests with the SQ3 "garbage freighter" theme as it loops and is then easier to work with. Considering only the theme (elec gtr 2?), I'm hearing this:
1st col. = Original, 2nd col. = Emulation
C3 B2 --> translated one semitone down
C4 B3
C3 B2
C4 B3
C4 B3
C5 C5 --> sound weird because not translated down
Bb4 A4 --> sound "correct" again as 1 semitone down
C4 B3
... ...
It looks like some tracks are translated like the one above and others are on tuning. Mixing the two sounds bad, as you could guess. Having a note slightly off like C5 in the above example happens frequently also and sounds badly "detuned" too, of course. I also noticed other volume problems, and at least perhaps one patch/sysex problem, in Kyrandia 1, the patch "Magical" (played just after sysex init. at the beginning) doesn't sound correctly at all.
Hope that helps.