Door fitment experts please 55-59

[hotrod1]

Trying to fit doors and have a problem with the window frame of the door matching the cab and need help/suggestions. This truck in not a restoration, it will be a hot rod.

The drivers door (#1) sits too low in the area in the pics. The entire door fits well except for these places.

There is a seam where the front cowl (#2) meets the window frame. Do you guys weld this seam or just take care of the misalignment? By the way, I rounded the door corner, so you understand what you are looking at.

The passenger door's (#3) window frame sticks out quite a bit.

Any suggestions on taking care of all this stuff?

Thanks in advance.