A few people asked for an update so here it is.
I called around got some other estimates. Although the work was underway already and I was on the hook for the charges I wanted to know how badly I was getting screwed. And boy was I getting shafted. All other estimates for the work were significantly less.
I went to the shop where my jeep was and raised hell. They basically told me i was fucked and the Jeep wouldn’t be released without full payment. I demanded an itemized bill. Easy enough to get. I also demanded the original master cylinder and that was difficult to get. Eventually they handed it over and I went and had it bench tested at another shop. Guess what? It was in fine working order.
While at the other shop that tested the master it turns out a staff member used to work where my jeep was getting work done. He looked over my itemized bill and was shocked. The best part? He gave me the contact information for the owner of the shop I was getting work done at.
I called the owner who was more than happy to talk to me and he was not happy about my situation at all. After explaining everything I wrote in my OP to the owner he told me he would take care of everything and quite a bit of retraining and ass chewing would be happening.
Within an hour my jeep was ready for pickup. After 4 days of back and forth with the shop. The two master cylinders deemed “defective” were fine and it was all technician error. The outrageous labor costs were reduced. He gave me back the master I purchased so I could return it. He had his employees purchase and install a master free of charge.
At the end of the day the store manager apologized and my bill went from just over 2k to 954$ and I returned the master cylinder I purchased for a full refund of 120.99.
I walked out with new front rotors, calipers, brake pads, a master cylinder and two new O2 sensors that I had purchased.
We did it boys. Thanks.
EDIT: COFFEE AND DONUTS HAVE BEEN DELIVERED