Modern automatic transmissions are extremely complex, typically beyond the capability of a local shop to rebuild properly. Your best bet would be a factory remanufactured transmission that carries a good warranty for both parts and labor.

However you are talking some pretty big $$$$ and need to take into consideration the possibility that despite being in good condition now you may well run into other expensive problems as that Jeep ages. Modern Jeeps do not have the greatest reliability or durability record.

I rebuilt my old '99 Ranger's transmission and I should have just gotten a remanufactured one. That transmission was only a 4-speed, 4R44E. I got my truck back a week later, and when the transmission was cold, it would audibly bang into 2nd gear and jolt the heck out of the truck. The rebuilder attributed it to a faulty valve body. It still did it when I got it back, just slightly less obvious. I took it back a 2nd time and the rebuilder put yet another valve body in. I got my truck back, and it still didn't shift like silk. Every once in a while, the transmission would shift before it was "ready" to, and the truck would shimmy just a smidge. At that point, I was tired of dealing with it. 

It lasted for 55,000 miles before the frame cracked. I sold it for cheap to a plumber, he's going to take the transmission out of it. He bought the same Ranger with a bad automatic and he's going to gift it to his son for his first truck. 

Rebuilders typically only warranty their work for 12 months or 12,000 miles, which is isn't worth the $2,000 I paid to have the transmission rebuilt. I found out afterwards that if I had chosen a remanufactured unit with a 5-year, unlimited mileage warranty, the transmission itself was only $1500. The company was trying to move those transmissions and they offered pretty good discounts. You live and learn.