Well I figured out where my problem is rooted with this door issue, so I figured I'd update this thread with at least a partial solution.
The root of the problem is in the part in the doorframe, not in the door.
(the top part in this photo)
The 2 screws seen there thread in to metal sleves which are embedded in some sort of plastic block in the doorframe (behind the B pillar plastic trim). It seems the bottom half of that plastic block is not attached as it should be which allowed the latch to slip out a bit towards the outside of the car. I took the plastic trim off, but couldn't really see a good way to get in there behind the metal and see what's going on. It looks nearly impossible.

Then again, I DID still have the driver's seat in which was obviously in the way.
Anyone know anything about getting in to that area of the car?
The temporary solution was to just loosen both screws and pull like mad on the bracket towards the inside of the car, and retighten the screws really tight in that position. it has held up for about a full week so far, but I'm sure it'll slip back out sometime.
AAAnyway.... I'm satisfied to have some sort of answer... Door shuts correctly for the moment.