Okay, since the old thread got nuked, I'm going to re-cap the current findings.

Right now, ZC's SPC APU is the cream of the crap. The best way to fix it is to just get a better one.
In the meantime, fixing AlSPC by taking the pitch down 50 percent (or one sharp note lower on a musical scale) ought to correct the pitching problem. Be SURE to compare the results with a sample of SNESAmp's output. If that doesn't work, then what sort of scale are we working with here?
Remember though that this still won't solve the muddy timing or lack of a lowpass filter.