That is what I've been thinking all along but they don't believe that is the answer. Been corresponding with him for the past few days trouble shooting. I have a 300SD with the same exact setup and purchased the alternator from him also for that car and there have been no issues at all.

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Current fleet-
2015 BMW 750i xDrive
2009 BMW 535i xDrive
2004 Chevy Avalanche 4x4
1993 Mercedes 300SD
1993 Mercedes 300SE (parts car)

Previous Benz's-
2001 Mercedes SL500
1983 Mercedes 300SD
1980 Mercedes 300TD
1996 Mercedes E300D
1999 E300DT
1984 300TD-T
1988 Mercedes 560SEL (parts car)
1979 300SD
2003 E500
2004 S430 4Matic
2001 E55
2003 E430