What do you think is the problem with my Jeep?

Also, the check engine light will come on when it starts missing and backfiring. It will crank up and run about 2 -5 minutes then go dead again and the check engine light will come on. The PCM gasket is still sealed no oil on it, just seems to be inside it and I dont see any, anywhere else. Also, when I am sitting still if I have the AC or Heater on, it will run hot and have to kill it and let it cool off before taking off again. What do you think this might be?

Again, if there is oil inside the ECM this needs to be addressed first, because it is most likely causing all of your running issues. The oil would not be getting in past the seal on the connector but rather traveling through the wiring just like water flows through the pipes in your house. When the oil is inside the wire shielding you may not see any exterior leaks, but if the ECM is filling with oil this is the only place it can come from. I strongly recommend taking it to a very well qualified shop that has seen something like this before. This is not simple easy repair. As I said before, you may be replacing the ECM and/or wiring harness to remedy that part of the problem.

Can I buy an ECM that has already been flashed? If not, could you give me an estimate of what it could cost, I know the ECM is between $300-500, Just need to know the flash estimate

Your Wrangler most likely has a security chip in the key that will have to be programmed to the new ECM, buying a pre-flashed ECM will not be an option. You will have to find a shop that can install and program the new module. And also make sure that the source of the oil contamination has been identified and removed. Wiring may also need to be replaced or you are risking damage to the new ECM.