Window and door issues

[Highwood Malibu]

So I have just put new rubbers on my drivers door. After adjusting the window, I can close the door by pushing on the window and it seals. But, if I try to close the door by pushing on the door itself the window never seals. I also notices the other day that the bottom of the door at the back of the door doesn't fit to the body, looks like the doors angle might be out but the from and top of the door seem to fit. Ideas? I also got the door hinge replaced a while back, that why I think its a door angle thing. Here is some pics, that might help

 

[565bbchevy]

I replaced both of my top hinges on both sides and aligning was kind of a pain and somewhat time consuming. I'm sure there is a proper way to do it but I just used a floor jack with a 2 x 4 a few feet long to hold the weight of the door and also wrapped a towel around the 2 x 4 for padding and since I didn't change the bottoms (which rarely wear out) I just loosened the bolts for the top hinge and pushed the door in a little,then tighten a couple bolts and check alignment and redo until you are satisfied.

 

[Pbngem]

Are those OEM 16" IROC rims?

 

[-83MONTESS-]

Looks like you mainly just need to pull the bottom out a little bit. When I put my doors on after paint I had to realign them which was fun.

 

[Highwood Malibu]

Are those OEM 16" IROC rims?

Added some paint.