Dead Short
 

Have an 87 MB 300D. Radio was popping occasionally and heater/AC was running intermittently. Replaced the alternator and both problems went away. But now the battery goes down over night. If I pull off the neg lead to the battery and then check neg pole to ground, I get 12 volts even after I remove all hot fuses.

I feel its a stuck relay somewhere but cannot find it, any ideas?

A bad regulator can drain the battery. If it started when you replaced the alternator, I'd start by unplugging the alternator overnight.