So last weekend I put on a new replace a top and the fitment was so bad that I didn't even post it to the what did you do to your TJ today thread. I had read that initial fitment can be a little disappointing but it should get better, it hasn't. My poor TJ looks like it woke up in and oversized shirt.
I think it is on correctly but the way it fits would say otherwise. I am 99.9% sure it is attached to the windshield header correctly.
some pics
I did this recently with a "Sailcloth" version of the replace-a-top. Fit perfectly. My best guess is that there is something wrong with your frame. If you're sure it's factory, is it bent anywhere? Or, in the process of removing the old one, did anything come loose anywhere, etc? Maybe some more pics could help.
Mine is a 97 with original frame.
Edit: Oops. As Jerry once said, call me a dollar short and a day late. Just caught up on the rest of the thread and see that this is resolved. And hey, I like your tan-colored cage padding. Where did you get that?