Update:
I figured I would post this so if any one else searching similar topics would actually get a conclusion.
So shortly after that second rebuild third gear developed a slight vibration in third gear, which could only be felt through the shifting lever. I brought it back the stealership and they said that it already has a new third gear and there isn't much more they can do.
I might have been born at night but it wasn't last night... Fast forward a month or so and the vibration is still there, intermittent, sometimes bad, sometimes not at all. It was only felt as feedback through the shifter. I was very frustrated with the whole situation so I started a warranty case/ customer service claim through Jeep/Chrysler. They said to make another appointment which I did. Jeep goes back in, I take two different mechanics for a ride and they both confirm the issue, but are bewildered to the fact it can only be felt intermit and when you rest your hand on the shifter... I was glad they acknowledged the fact it was doing it. They said they had to contact Chrysler to see what they could do about it. I asked if they could just replace the whole transmission and they said Chrysler would probably not authorize it. I re-contact my warranty case worker and he says they need to look at it again for a more in depth diagnosis. At that point I became even more frustrated, knowing this transmission is having issues and things are not right. It was rebuilt twice and I am still having issues, however minor I believe they will become major with time. So as the warranty case worker states I make another appointment two weeks out for further diagnosis. During those two weeks prior to my appointment third gear goes away!
Case worker was advised along with the service manager at the dealership. I tell both I have a sneaky suspicion that the third time is not going to be a charm and the transmission needs to be completely replaced.
Fast forward to the second diagnosis (third gear no longer exists) and the service manager says they will probably need it for another week or two to get the transmission torn down, order new parts and rebuild it again.
My fuse was non existent at that point and just about have a melt down. I told them I am not going without a vehicle for two weeks and this transmission needs to be replaced which should take no longer then a day. Service manager says if Chrysler authorizes it they will replace it. I told them the warranty case worker said they are going to do whatever necessary to fix this problem once and for all. I told them IMO that was a whole new tranny, no more poor rebuild games.
Fast forward to my appointment a week later and the transmission is replaced, I am provided with an extended full warranty, service plan, road side assistance, and a bunch of extra stuff for 6 years 85K miles. Which should last for ~3 more years. If my wife's Jeep (exact same just two years newer) requires any warranty work what so ever I get it for that Jeep also.
Three Cherokees (XJ), Two Wranglers (TJ), and one Grand (ZJ) none with less then 100K and most close to 200K and no issues that weren't self inflicted. I reiterated that fact many times and when vocal about the situation through several different avenues it was finally fixed, the way I wanted it fixed to begin with.
In the end, mechanic said that jeep has been having problems with bearing quality but they specifically haven't seem any issues because they are a small dealership. My guess is the bearings really were bad the first time, then replaced with ether more bad bearings or bad quality control on the rebuild. It took me forever for them to get it in with the second bad bearing go around and I think metal flakes were then swimming around the tranny compounding other problems. Second rebuild missed some parts, or other parts were adversely affected from issues. Swapping one gear and not them all lead to a wear/ meshing issue which caused the feed back and vibration. To me that was not acceptable. I wanted it to be smooth new which in the end I finally got.
As far as the service plan, extra blah-blah-blah, they probably gave me what they are authorized to give any one in a similar situation and overall I am satisfied. I hear horror story's of every brand and truth of the matter is quality and service from mainstream dealerships and manufacturers is not what it once was across the board.
Unfortunately I live in the rust belt and vehicles 10 years old that are driven during winter are almost no good. Frames rot, lines rot, floors get holes in them etc. It is what it is I guess. I have a good job, nice home, and am very happy where I am so moving because of rust isn't an option!
I have been a hard core Jeep owner for many years and this is the worst issue I have had. In the end it was fixed and all is good.