If it's a factory top and the back was overhanging it sounds like a different year top. The early tops had two alignment pins (1 per side) and the later tops had 4 (2 per side). What you need to do is drill new holes in the rail to accept the alignment pins. Some people actually just remove the pins from the top, but I don't recommend that.

Also, the front gap could be from the footman loop changing positions on the windshield header. Qtec sells a kit to move it which includes a couple of nutserts and bolts and a new trim piece for the header. You re-use the existing loop in the new location.

Other than that, I'm not sure what is going on without pictures.

 

It wasn't factory, it was smittybilt.
In hindsight that should have been another red flag that it wasn't going to work.

 

I am not familiar with the Smittybilt top but it could be the same issues.

 

Not questioning your intelligence, but did you remove the door surrounds and all associated soft top parts?

 

I checked for and removed everything that was associated with the soft top before attempting to put the hardtop on.

 

Then you should be good.

 

I am near PGH.

 

Still have the hardtop?? Pitts like 10 maybe 12 hours for me... Plus a couple friends up that way I need to visit. How much are you asking for it?? Also, is it the std one piece? Or the freedom?

 

I see them pop up in Craigslist auto parts section in Austin regulary, so I would guess even more frequently in Dallas with the larger population. Also, see if there is a FB group for Dallas JeepPeople like there is for other cities and ask on there if anyone has one they want to get rid of. Many of the older JKs came with a dual top option and people decide they only want to keep one or the other and not both.