[lks dcvn]

You are making good progress - let's start there. Once you dive in - you can only improve on what you started with.

Starting with the top on and replacing the body mounts is the absolute right process - w/o this - you would be in a tough spot to get things back to factory spec.

I've done this a few times so I'll explain my process (or at least my approach).

- Steps 1 & 2 are bolting the top on in factory holes and replacing the body mounts and bolts.

-Part of this process is taking note of where the shims are at each body mount position, which it sounds like you have.

-If the old bolts were hard to remove and the rubber mounts were toast - there is a high chance that they are factory originals. Mine have usually been welded to the floor as a special treat to me, which also sounds like it was part of the factory body mount install process.

- When I do this - I have not removed the doors as I like to shim until the doors open/close w/o sticking at the B-pillar. It sounds like you may have done this to replace a bad hinge. When I remove hinges, once they shut well, I usually drill a hole in them (through the a-pillar) as a guide for when I put them back on to help with alignment.

- the B-pillar (rear bedside is a fixed point) - I line up my doors and gaps to the b-pillar (latch) and then worry about the front sheet metal second.

- I have done this a few times and have never witnessed a smaller shim in the body mount replacement - it is usually the thick metal square shim. That doesn't mean you can't use whatever shim you want to get it lined up.

- When I have purchased the LMC body mount kit, It comes with a 'star washer' that goes between the bolt head and the cargo floor. It helps pull the carriage bolt down to the floor and prevent spinning of the head while being tightened. I have only seen them sold with the LMC kit. The rear-most body mount has a metal piece that matches the ridges in the cargo floor.

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Now looking at your pix (without hearing/seeing how the doors close) - I would line up your doors to open/shut cleanly at the b-pillar first. You may even consider taking off the front clip to focus on that as they will continue to rub. You don't know if the prior owner ever moved around the front metal so don't consider it a reference point.

You now have enough 'clean' data points to do this - top is on (OEM reference point) body mounts are solid (not sagging), door hinge replaced/repaired (not sagging), shim count at each body mount location to reference. With these the things left to tweak are the latch on the b-pillar and the hinge bolts for the door - way less things to adjust.

* Door gap tolerances from the factory were not perfect - so with that said*

Your door gaps on the driver side look pretty good and match the body line - I would move the door back toward the b-pillar if possible or move the fender forward toward the headlights to alleviate the rubbing.

The passenger side - close on the top, open at the bottom. Could be a few things
- door is hung incorrectly (appears higher in the back - so runs uphill to the bedside (also likely why it wouldn't shut when shimmed - it was already too high)
- weak metal in the pass side floor (floor mount, support under floor, a-pillar where door hinge bolts in)
- fender is hung incorrectly - appears to run uphill toward front of truck.