So is the door lower now than it was before you replaced the pins & bushings? Is there still up & down play in the hinges if you lift up on the lower back corner of the door? How did the bushings fit in the hinge...did you have to tap them in place?
As far as "tricks", not the correct way, but a way if you have clearance at the lower rear corner of the door to cab corner is to install a shim...1/8" should do, between the hinge & the door on the bottom 2 bolts on the lower hinge...this will raise the door in the way that you need it without fighting the bolts on the cowl.
There are "S" shaped wrenches for the hinge to cowl bolts. They can be with a bit of effort with an off-set box wrench or a homemade shortened 9/16" socket welded on a flat bar. Hope this helps ya', Lorne