Charlie, I don't know what to tell you - trying to digest this! It may be an issue with your Auber, but hard to say. Curious - did you try the 120/600/800 setting that Auber gave you, or did you just go straight to the autotune? Might be worth a shot, if you didn't.
Water pan above the smoke box: I know the "flavor saver" box has hooks, but I strongly discourage anything between the meat and the heat. I know it's not very big, compared to a #3 rack, but you'll get the best moisture by setting it on the floor, right up against the smoke box. It will do less to block/channel heat than when it's above. Minor issue, but you'll find that's pretty much the universal consensus around here. Are you using any other drip pan below your meat?
Regarding brining: I agree that you certainly don't have to brine everything, or anything, for that matter! Personally, I find the difference in butts, loins and poultry well-worth the effort. But, many folks are plenty happy with the un-brined results. Is what it is, and a matter of choice.
I think you should test your element by undoing your bypass, and check the temps with the stock controller. Set up the smoker with your heat sink (not empty), run it at 225, and 250, and monitor the temp swings. Those swings actually average-out to your set temp, and we have all produced some great BBQ with those "swings!" By the way, your friend's Cookshack, with the "digital" controller, works the same way. It is not a PID controller, and has the same temp swings as your stock controller...it just displays the set temps digitally. We have a CS test, by an owner, that proved that.
After testing that your element, indeed, heats the box properly, it'll be time to run a few tests on the Auber. If you'll humor me with the stock controller/element test, I bet we can figure this out. It's a process of elimination!