So, I'll shortly hit the magic 3/36 for bumper-bumper and figured it was time to finally take care of the recalls.
Amusing that I had a couple of the chronic, well-known issues and they dismissed them.
It's not like they're big issues, just things I figured to have looked at before the warranty goes bye-bye.

Steering column clunk: didn't notice anything
Freedom top leaking: crank on the screws
Intermittent P0405 code: found stored code, but could find nothing wrong

They did agree to replace a rear lamp that had a problem with condensation inside the lens.
They also replaced the stripped handle on the seat height adjuster. (I think I used it maybe once, when it was really hot out.)
Reprogramming for the trans oil temp recall, plus some newer ECU flashes to help with sluggish acceleration lately.

In all, I guess I can't complain too much.
They were friendly and didn't push (too hard) the dealer services.
No grief about the mud "paint" inside the engine compartment, added door locks, added rear gate stay, or the missing interior carpet with mud lining all the cubbies and corners.

 

Here is the good thing for you. My experience as a dealership tech (not Jeep) has been this, if you complained about a concern and it WAS NOT FIXED/FOUND while UNDER WARRANTY you are entitled to the repair even after it expires! I would suggest going for a ride with the tech and have him feel and hear the clunk, I will be going through that soon with mine.

Now I can't say they'll warranty the top leak, but go complain about it again before the warranty is up. Then it is a return complaint and you have more ground to stand on.

Just my 2cents

 

Brought the JK in for one last warranty fix 35,960miles. I've had the clunky steering for a while now so I wanted to get it looked at, I also wanted to get my ball joints checked. I bought the JK new in August 08 and have not gotten it inspected until today. I figured I'd hold out to get it inspected until the last minute so the dealership would inspect everything and replace the worn/broken items on their dime.
Turns out everything checked out fine even the ball joints, the only things they found was worn upper and lower steering intermediate shafts (replaced under warranty). Clunk is gone...for now. Ask them about this....

 

Just the other day someone at work was telling me a story about this other employee having an issue with his Explorer's transmission as the warranty was nearing expiration.

He took it to the dealer and they said they would need it for several days. He was about to leave on vacation with the Explorer so the dealership said that since he had come in before the warranty expired he would be okay.

He went on vacation and went back to the dealership when he returned. They fixed the transmission and told him to pay the bill at the cashier's office. He said it was suppose to be under warranty. They said his warranty has expired. He is over the mileage so Ford wouldn't pay. Cost him $1500.

He might of had a chance if he had gotten a receipt for the initial complaint. That way he would know it is in the system.

 

I got the Jeep back today and they documented everything I requested them to look at.
For the "not found" problems, I'll have the proof it was reported before the 3/36 expired. (like I expect that will do any good, but it's something)

As for the well-known steering column clunk, they ruled out the obvious clunk because I have quick disconnects on the swaybar links. Any noise or clunking felt, they said, was due to the disconnects. (even though the clunking existed before I installed the disconnects and the clunking is a common, well-known problem)

 

This is very good advice, I rode with the tech and we took an interstate off ramp where, I don't care who you are, you gonna feel the clunk and he did.

 

Got my intermediate shafts replaced yesterday. I got lucky because when I told them about the clunk the tech happened to be standing there and said I'll go get the intermediate shafts.
He checked everything else, which I had already done before, and said everything was tight, no movement from the steering box on.
Maybe you could try a different dealership, even if you have to drive a little bit to get there. Some dealerships are just plain lazy and worthless while others are more than willing to help.