So I have your typical alternator whine. Funny thing is it's only in my right rear speaker. My first attempt to kill it involved opening up my Empeg (Mk 2) and reseating all connectors. I examined both the docking connector and the two mainboard connectors to see if any pins were loose, etc. None were. I buttoned it all back up and the whine was gone... for two days. Now it's back. As bad as ever and still in only the right rear speaker.

Any suggestions as to what I should do next?

Cheers.

Hmmm... A Mark2 with a Mark2 sled? The fact that you were tinkering with the player, testing various things, makes me think it is a contact on either the player or the sled. The early Mark2s had trouble with the pins (for lack of the proper term) coming out of the wiring loom on the sled. Perhaps you have a loose contact there? It would mean pulling the sled to find out, though...

As Paul G said, check for this problem.

There is also the chance it might be an intermittent problem with the amp. See if you can rule out the player by unplugging the RCA cables from the amp.

Check to make sure that the disk drive IDE cable isn't scraping up against any components inside the player and getting rubbed raw.