I had similair problems i am also using a two inch body lift and one inch poly bushings so my cab is sitting that much farther off the frame. On the drivers side i had the same problem as you i ended up cutting slots in the mount on the frame, bent it up untill the new mount was flush with the pillar. I made a backing plate for the frame mount i cut with a run off tab and cranked the heat on my welder. The polyurethane was soft enough i could make fine adjustments on the cab to level it out just by loosening ot tightening the cab bolts a little. The cab mount on the passenger side sat perfect against the pillar but i had to throw a couple washers in there to get the cab height the same on both sides. I also took my measurements off the floor to the pinch weld that runs along the bottom of the step. If your truck is on a level surface measure from the ground up to the frame rails, the mounts coming off the rails and the pinch weld along the bottom of the step. Also check tire pressures a low tire can really screw things up for you.

 

New cars are supposed to be a 3mm tolerance when making structural repairs. Have you noticed how much adjustment the give you in the mounts on the frame, these trucks aren't perfect.

 

I didn't take any measurements from the frame itself. I'm thinking my best course of action would be to remove the step plate backing and slide it up towards the dash 1/2". Just hoping I don't trash the step in the process trying to break the welds from the backing plate to the step itself.

If I move it up then the cab mount will line up under the lip better, the floor will be slightly higher but it won't be noticeable.

 

Measuring from the bottom corner of the dash to the floor ive got 18 3/4 on my truck. What i was saying about measuring to the frame is measure from the ground to the cab mount on the frame and make sure its the same distance. bolt the new cab mount down with the bushing in. Now using a jack on the front corners of the cab or some blocks of wood level the front of the cab out untill you get the same measurement on each side of the cab. That piece you replaced below the hinge is set by the hinge bolt and the step sits against that piece. The only thing i can see from the photos is the piece below the hinge looks like it could be pulled back which would give you a gap and allow you to raise the step a bit mine was 1/4 off side to side so i split the diffrence when i welded the cab mounts in. In the end if all the panels line up 1/4 on each side is nothing. Ill go out and measure everything if you need me to. Back to the frame if you have a low tire and it puts a bit of a twist in the frame or the ground is uneven, or even if the frame is off a little ladder frames were not the best design ever. This can really throw your panel alignment off. Could the dash be lower on one side?

 

Ive got 5" from the step to the floor and 8 3/4 from the floor to the bottom of the vent opening. Both sides

 

At this point it might be a good idea to put the door on and check the gap at the bottom see waht the rocker is doing and make sure there isnt any pressure on the gasket. You never know maybe the gap at the front of the rocker will be huge and it will show you that everything does need to go up.

 

It was in the mid 90s here but I managed to get it done over the weekend! I had to break the welds on the step backing plate and move it up. I had failed somewhere and it was indeed welded below the 5" mark by about 1/4". I moved it up to 5 1/8" and got everything clamped in place, then I welded it all together! Got the floor pan in and repaired the section under seat that was rotted. Whew! Now for the toe panel and then on to the other side!

I did get the door on after I had it clamped up and it lined up pretty good. The top of the door seemed to be "in" a bit more but it has no gasket and I didn't spend a lot of time lining it up once the door closed well.