Holy crap that was it! Thank you
@XianXi! I swapped the position of EPROMs for V3 and V2 and the sound issue is gone. I mean, I did swap out every single part and verified every single EPROMs to make sure they weren't bad, turns out it's just the splitting.
Looking back, the pictures from Mike McBike that I used as reference for the jumpers showed it clear as day. V1 = v1.1 V2 = v1.2, it was right there. I guess I won't make that mistake again.
Thanks again XianXi. Also thank you everyone else who helped me troubleshoot this as I stumbled along.