It's been months now since my buddy and I fixed the issue and everything is still running amazingly guys.
If EVER you get a weird 'no communication issue with your ECU or Transmission, head straight to the ECU boxes and investigate.

Also, rebuilt alternators are garbage. my buddy pulled mine apart and he quickly realized how cheaply 'repaired' they are. He ordered new military spec parts and installed them and my alternator has been awesome every since. I had nothing to do with the battery at all. On the E53 X5 we didn't have a choice of selecting different batteries in the software he was using so we went straight to the mechanical side of things and fixed them.

Now we're looking into fabricating a set of headers for my engine based off of special header calculating software that takes literally everything into consideration so it's going to be interesting. Wish me luck.

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If you can still see the disapointment on his face in your rear view mirror, he's not far enough behind.
98 M3 Sedan blk/blk Sold
00 BMW 540i Sold
03 BMW 4.6IS
98 BMW E36 M3 modified