Just a thought...is your windshield angle adjusted right? If it's off, it can throw off everything. I don't remember the exact dimension, but you measure from the windshield frame back to the rear edge of the tub. I'd check it.
+1 - don't cut on the hardtop at all.
+1 - adjust the soft doors as needed
Use weatherstripping to shim the top up if it will help your interference problem. A picture of the door installed would help.
My Ammo Can Console: http://www.jeepforum.com/forum/f12/yet-another-ammo-can-project-finished-1498520/
My 8.8 Swap: http://www.jeepforum.com/forum/f12/yet-another-ford-8-8-swap-extras-1565339/