Current top situation updates and advice for any who are getting a replacement top from Jeep.
Since the original replacement/screw up was installed, I have been back to the dealer twice. The first return was a good deal of adjusting and measuring which ended in the ordering of a new top. They replaced that the day before yesterday and it turned out the exact same way. VERY tight fit, pulled up on the front edge of the header, back window stretched, sunrider would not properly fold down and lock. Yesterday they tried a third top to no avail.
Knowing quite a few folks at the local dealer, including owner, I was allowed to go in the back to watch and assist. Parking a brand new 2016 next to mine, tops and frames were removed, measured and compared. Phone calls were made and such. It was determined that the recent tops being shipped are cut too short to properly fit on the JK. I am unsure of the JKU. From what the service manager told me, it seems there was an issue with tops stretching and becoming loose inside of a year. (Mine was coming loose and flapping at about 8 months.) He stated that due to this, they have changed manufacturers and the tolerances were reduced too far, causing a shorter than required top.
Not having witnessed the phone conversations, I can only take his word on the cause. I can tell you that 3 brand new soft tops did not fit. Jeep is working on a solution for me but there is no time frame when it will be completed. If you need a top replaced under warranty and the dealer needs to order one, you may encounter the same issues. I will be purchasing a Trektop NX or the Smittybilt Combo Top Friday. Yeah, Smittybilt... I like the window storage built into the roof for easy access on trails.