Somewhere there may be a dead short where current is slowly making contact across a bad connection positive to negative--my guess is in wiring somewhere. Not sure if the S-Class vehicles were involved in the factory main wiring harnesses fiasco of falling apart insulation which caused things like shorts. The problems with the harness were definitely during your year, though. The other idea I had is the CD-Changer. Of course, if you disconnect all fuses, the changer should have no power. Check to make sure it doesn't have independent power to it anyway. On my Range Rover the battery will also be dead in 3 days due to the CD-Changer "remembering" the position of the disc.

__________________
________________________
2002 Mercedes-Benz E320 4Matic
1995 Mercedes-Benz E320 Wagon
2005 Land Rover LR3 V8 SE
1999 Audi A8 4.2L quattro