Brake Disc Caliper problems of the 2012 Ford Mustang

When I first purchased my car I started to notice that shifting didn't seem right. One morning I walked out to my car to start it and the clutch was on the floor. I pumped the clutch several times to get any kind of pedal pressure back. This happened one more time and I did the same thing the get pressure back. On 6 Dec was the first time I brought it in to a Ford service dealer to have it looked at. But before I got to the dealer, I started to notice a lot of noise from the transmission. The noise sounded like a whine. Then noises also came from the rear brakes I started to hear a lot of noise from them, like they were still touching the rotors. When I got to the Ford dealership I told them about all the issues I was having and and left the car with them. Later that evening the service center said the car was done. When I picked it up the same issues were happening with the transmission and the brakes. I returned to the Ford service center and dropped off the car again the next day. The service center keeps on saying the transmission and clutch are fine, everything is normal and there are no other reported issues with this problem on the transmission. On the brakes, the service center did find that both rear pads had broken guides on them and they were allowing the pad to move around in the caliper. The service center fixed the brake issue and I haven't had anymore issues with that. Now on 10 Dec, I left my house and went to put the car in sixth gear and it wont go in, the gear will just grind. I pulled over and went through all the gears and sixth gear will not work. I have contacted my local Ford dealer and service center and have yet to hear anything back from them.