I know you said you re-worked J101, but if you're in the mood for trying something that probably won't hurt and don't mind possibly wasting 5 or less minutes....
This might sound odd, but try removing J101. Now, re-install it about 1/2 to 3/4 of the way on to the connector pins and do a cold start. Does the game run ok now? I found out my J101 connector was causing some resets one time by doing this; the tarnish was preventing a perfect connection only when the plug was 100 percent on, because.. well that's where you are supposed to push it on until. (edit - when I pushed it on less than all the way, the untarnished area of the pins seemed to make a better connection, and things were fine... just indicated it was time to replace that stuff)