2005 E320 CDI - 260k miles
I'm going to try to keep these issues separated for sanity purposes.

Issue #1 (been happening for a long time)
Conveniences went away(frequently) and my battery would be dead in the morning (rare). The conveniences went away intermittently at first, but then became permanent. I knew I had a voltage issue. The car would idle with 12.6-13.2V and then once I got going the voltage would read 13.8-14.2V and stay that way even during a subsequent idle. I learned that the Voltage Regulator is a common and easy replacement, so I completed that with an OEM Bosch unit. It seems to have made the situation better. My permanent convenience issue is slightly less permanent, but still very much present. The voltage issue remains.

So, I tested and replaced the AUX Battery. It was 9 years old and DEAD, even after trying to charge it overnight. Main battery is tested and is good. Problems still happening.

Next, I'm guessing my alternator needs replacement, but it seems strange that going down the highway, I'm getting 14.2V so it's at least partially working.

As for fault codes, I was getting 9055 which is a BCM error, but it's a stored error that I believe was caused by the AUX battery. I can no longer reproduce it after I replaced it. I'm also getting P1856 which brings me to issue #2...

Issue #2 - Transmission and Starting (problems started this weekend)
Symptom #1 - Frequently I cannot start the car. I turn the key and nothing happens. I turn off the car and wait, and try again. Over and over until it eventually starts.
Symptom #2 - The car drives like when the clutch is bad on a manual car. The engine revs high and the car accelerates slowly
Symptom #3 - The gear display in the dash shows the incorrect gear. Sometimes it's blank. The C/S button doesn't toggle between modes
Symptom #4 - The transmission doesn't switch to a higher gear. Stuck in a low gear
Symptom #5 - Can't shift into R or P from D or N. Have to take foot off brake to be able to overcome this issue
Symptom #6 - Car in gear(according to gear selector) and engine revs like in N. No movement.

All of these issues seem to get resolved if I turn off the car and wait and restart. Not cool when I learn I can't get past 3rd gear on the interstate and have to pull over.
I tested Transmission Fluid level and it is fine. It's never been touched. The only code I'm getting is P1856 which is the selector lever module.

Is this clearcut? I just replace alternator and selector lever module and I'm back to normal or is there something else going on? Should I replace the BCM?

Thank you