Finally had the chance to run some more extensive testing based on
@Mitsurugi-w 's tests and advice. I took a multimeter to the jamma edge of my super gun, which is an Axunworks Control box. I have the optional jamma extension for it that has a voltmeter on it. The voltages on the jamma edge did not match what the voltmeter was reading (5.10 vs 4.98 or 89 via multimeter on the edge, I can't recall exactly). I shouldn't have been surprised to learn, after reasearching, that these voltmeters are commonly not very accurate and require calibration. It appears that I've been undervolting the board during my more extensive testing. I will say, this is all testing I did AFTER I got my board back from Cruz with the replacement cable and Simm3. Before I ever seny my board to him, these problems were present in a variety of testing environments to different degrees (in cab, different superguns, no a/v mod, post a/v mod, pre/post buffer chip replacements, etc). But I am relieved to say that after adjusting my voltages (to a consistent 5.0) I'm almost never seeing the sprite glitches. Occassionally third strike will boot with them, and new generation does as well. But everything else seems to be working okay after switching between games and testing. Tested the board in a couple of my cabs as well and didn't get any sprite glitches yet.
Sorry for the headache everyone. Shaking my head at how easily I overlooked the voltage discrepancy. In any case, I appreciate all the help and advice from the community.