First- I hope your dog is OK. I would rather my jeep burn to the ground then to have family/ girlfriend/ myself/ including my dog...in ill health.
You have gotten some good/ very necessary repairs done already- So at least there is hopefully not much else to go wrong. I am still dreading the day that I have to have my clutch (TSB) and throwout bearing (TSB) repaired, and possibly the rear main seal eventually.
That was a great idea to get the extended warranty. Even if you have more problems (God forbid)...or if you ever decide to sell it, you wont have to worry that no one will want it due to some costly issue, and if you keep it then your a$$ is covered till 76,000 (?) miles now.
It seems you were lucky to get the extended coverage at 37k + miles. I thought people were out of luck at exactly 36k.
Be glad that you weren't turned away from your dealership due to a bunch of modifications. Lots of people are having to battle dealership service depts for warranty work, due to this.
They may decide to just throw a new transmission in it. They have done this before rather than taking it apart time after time.
Eventually, they will develop a seal kit that actually works. TOO many people are STILL having this leak issue as well. Just a matter of time. ( And thank God you don't live somewhere that gets a TON of rain. I know that one is really a PITA. But don't give up hope.
If you use your jeep on the trails, articulating and such, then there is no other/ better solid axle/ upgradeable 4x4 on the market including the Hummer and the FJ. Just look at some of the youtube Hummer videos out there. They have a lot of problems getting down the easiest of trails. Plus you cant just pull the doors and top off of a Hummer or FJ.
Don't have any comment on the loaner car. That just sort of sucks.
Hope some of this helps...Good luck. It will work out one way or the other.