First make sure the hinges aren't bent outward, the tub is square, that the frame mounts are in good shape, and the "B" pillar is not rusted/rusting out at the floorboard.

Heat the Nader pin with a propane torch. That melts the thread lock. Then you can loosen it with a (IIRC) a 50-torx socket. Loosen enough so it can be moved with a light hammer tap. It floats in a captured cage. Once loose, you can move the Nader pin in, toward the center of the tub. Then tighten.

The thread lock will re-set as it cools, so you've got to move quickly.

 

The tub is square, and the B pillar is in good shape. I will have to look at the hinges though, not sure if they are straight or not. It is odd that my stock hard doors are flush so I 'assume' something is amiss with the new half doors. The hinges on the doors are the Wrangler stock hinges, and the ones on the body are the stock CJ7.

I have moved the pin towords the center of the tub but it only moved about a 1/4 inch at best.

Thanks Leve

 

Another photo from the hinge side

 

I'd next look to see if the door frame is not warped...

 

It's really hard to tell from the pictures, but check to make sure that the bottom of the door is not too low. If it is, you can loosen the hinges on the door and adjust them so the door is higher. I just installed some half doors on my crappy tub and I ran into this same problem. Adjusting the hinges and the striker pin worked for me.

 

It does appear the rear of the doors are sagged a bit and possibly interfering as Russ said...

 

It does appear that the rear of the door is a little low. Loosen and adjust the hinge halves on the door, NOT on the tub or the full doors won’t fit right.

Before you do anything, remove the upper half doors (the window portion), adjust the door to fit the body and then deal with the uppers. From what little I can see in the photo, I don’t think those uppers are compatible with that top. Those look to be the uppers for the OEM YJ top frame and will not work with any other top.