Door alignment and body shims

[bigdon-70blazer]

I am putting on the doors and while putting on the pass door, I am having alittle (understatment) problem. Seems like I am having grief lining it all up, but that is same for all guys who have done this kind of resto. I seem to be fine at the bottom edge and back seam is pretty good, front ok, close but ok. Having problems with the back edge at the top, seems to be off of the rubber rest about 3/8 inch but i can push it closed but I am thinking that I will have to slam the door shut, IOW it won't fall togather easily. Also the ridge at the lower part of the door is not strait. Now when I took the body off, I braced it and replaced the old worn out body mounts with new rubber ones from LMC and I replaced the shims EXACTLY as I removed them. I thought that would be adequate. Any advice???