I doubt it's the connector on the back of the empeg.

What is more likely is that there is an electrical fault in the box: bad sound like you are describing implies a poor earth somewhere. You seem to have a lot of problems with this player: is this the one that had all the mods done to it? I am beginning to question the quality of the work you have had done.

I would suggest you dismantle the unit and remove the main board. I would then make sure your memory board is 100% insulated from the case. Clean the case screw studs and the points where they come in contact with the board on the main board. When you re-assemble it, make sure that the screws are properly tensioned/torqued to ensure good contact to the case. You should tighten the screws until they first resist turning ("finger tight") and then turn them just 1/6th of a turn further.

I found that the screw at the rear of the board near the RCA connectors can occasionally come loose, and has caused odd sound problems (alternator whine, crackle, etc.). This one is either lathered with thread lock (can eventually cause a poor contact) or has none at all (comes loose and a bad contact occurs).

There is also a resistor near the RCAs which occasionally goes bad leading to crackle on the front channels, which just needs re-soldering to restore the sound. It's either R73 or R74, which are 0 ohm links to ground, mounted near the RCA turrets at the back of the board.