The problem turned out to be a few incorrect register settings for DDR3 configuration. We regenerated the registers using the Excel aid, and now the board is stable. (Several boards running for several hours) Surprisingly, with these few registers incorrectly configured, the board sometimes functions as much as 4 hours without a problem!
As for the PMIC configuration etc, I am not an expert on this so I'd still appreciate your comments and thoughts, but here is my educated guess: I don't believe you have to change anything on the Linux side in order to have a *functional* board. I believe you must do the changes to Linux side, only if you want to make use of all power saving, frequency scaling, sleep, shutdown etc. features properly.
I say "educated guess", but I am slightly more confident than that, because I have proof that you don't need to change anything, because I have functional boards. My guess is that even if you completely disconnect the PMIC I2C, the board would still be functional.
Your thoughts? Am I missing anything?
Best regards,