I guess I just needed a couple hours to step away from the alignment issue...
Kevin, I took your advice and moved the door upwards and out at the top to get the front moved up. While doing that, I noticed that when I put pressure on the door to open it, the inner hinge body hole would line up with the pocket nut thingy. So, got a bolt in there too! Still had the problem of the door not shutting very well and found that I never tightened the lower hinge back bolt so the hinge arm was hitting it and causing the whole door to warp when closing.
Phil, I took the back bolts out on the passenger side to see if it made a difference and it doesn't make an alignment difference. I noticed a bit of flex at the pillar though and the door feels *lumpy*? when it opens and closes (don't know how else to explain it). The inner hinge bolts installed seem to stiffen things up a bit. Also, there is a noticeable gap between the pillar pocket and the back of the hinge body so I didn't give her the beans when tightening them. I think they are just there to reduce flex/twisting maybe kind of? I would assume that the later models have a bit more support at the pillar so possibly they aren't necessary.
Thanks for the help guys, the doors are now aligned and closing great! Now on to more body work which I despise.
