Your missing drive problem is almost definitely the cable. If the player is under warranty, support can send you a new cable or take the player in for repair.

The power loss issue is either a wiring problem (perhaps a loose wire on the docking connector, that has been known to happen), or simply because the empeg is more sensitive to dips in power than your average CD deck. It is a computer with hard disks, after all.

The problem with the Aux-in on your CD player is of course not the empeg's fault, that's just Sony being tight-assed about the CD-changer interface. What you want to do is wire them the other way around if you can: Send the Sony into the empeg's aux-ins.

Question: How is the Amp Remote Control line connected? You have two of them at this point, the CD player and the empeg player. You're not connecting both of them together are you?