it's no secret. every single location that could possible leak has leaked for some poor soul. gotta go through them one at a time. Some of the oft overlooked items are the HVAC seal, window seals, and cowl drains.
the 6th digit indicates the trim level and yes, a 2 means base. but since you could order just about anything on a base, that alone doesn't mean much (as your truck testifies since it is simply decked-out with goodies!
if I was closer I'd swing by to lend a hand. it's really becoming a problem child.
But I too had plenty of setbacks when I built mine and it was all worth it when I finally got to drive up the trails in Moab. don't give up! focus on the goal line! think about how awesome it'll be to drive around in it knowing you defeated all its demons and came out victorious!