After several hours of messing with it I cut it loose from the fixed body mounts on the sides to see how it would sit. Thankfully I had bolted the body mounts in place vs welding, because it became apparent that they were in the way. After another hour of fussing with it I coupled together an extended pipe clamp that allowed me to flex the top in to fit the body and found that the two fixed mounts needed to move forward.

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The drivers side measures 1" while the passenger measures 3/4" so I think the answer is to shift them both forward 7/8". Instead of being back from the door edge 3.125" to center of hole they needed to be 2.25". Not sure if it's a difference in the body or just a feature of the top but I'm on the path to getting it fixed. Wish I'd waited to do the body mounts until I had the top in hand and it would have saved a lot of frustration. The back edge is still sitting high by about 3/8" to 1/2", but I believe the key to that is getting the body mounts fixed, then using the windshield angle to "tweak" the top around those fixed points. At least that seems to make sense....