Mike, make sure the windshield affixed to the Tub is dead-straight on in relation to the tub. It' GOT to be square, there's not bones about it. You've got two points to be concerned with:
1. Squarness of the Windshield Frame to the tub.
2. Squarness of the Hard Top mounts to the tub.
If these two things are true... then the doors hinges and the tub hinges should have enough slack in mounting holes to align correctly. I can assure you that then about the only point that you may have problems with is the top door frame to windhield seal and that's easily cured with some sticky backed foam insulation.
What I did was the following to mount the Hard top and the windshield frame.
1. Roll into the garage.
2. Mount the Hard Top the Tub.
3. Using a Plumb drop the line to the garage floor from the tip of the Hard Top, driver side.
4. Mark the floor with masking tape and precice marking pen.
5. Do the same on the Passengers side.
6. Pick a point on the rear of the tub and the rear of the Hard Top to drop a plumb bob from.
7. Mark the floor as in step 4, for both passenger and driver sides.
8. Drop a plumb from the firewall/fender seam to the floor, and mark it.
Now you have a pretty good understanding if the Jeep's "square" by measuring from the firewall mark back to the rear tub mark ( I used the seam on the rear corner to rear quarter panel). If the tub's square, then it's a good base to lay the Hard Top upon.
Now measure the points from the front of the tub to the windshield. Are both the driver's and passenger's equal distance from the firewall? They should be.
Now measure from the firewall mark back to the rear of the Hard Top Mark. These measurements also should be the same.
Once any inequities are corrected then, and only then do you hang the doors.
I'd not suggest moving the Jeep a bit while these meausrements and corrections are being made. It can become a lenghty and prolonged correction process but is greatly shortend because you now have some starting points and metrics. I really prefere using the fire wall as a starting point. You've got to assume a starting point, and that's about the best place I could think of to start.
I'v you're really anal about this, when you're fished you could drive the Jeep out, and measure width between marks and the length between the marks and then get out your slide rule and have great fun checking for squarness. Though that's not for me, some people love that kind of stuff.