Here is a final update on this issue. I also had a squeaking noise coming from the rear passenger side as well that was look at. The squeak would only happen in the cold weather and I though it might have been in the rear suspension.
I took my mustang back to the dealership I bought it from one year ago. They addressed both issues.
-The leak was caused by a bad seal in the urethane on the rear window. They ended up ordering a whole new rear window from the factory and had a third party install the glass at their shop. No more issues.
-The squeak was being cause by the rear passenger seat latch. An adjustment was made (not sure what) and the noise has stopped.
I took the car into the dealership on November 30th, 2017. I did not get my car back until December 31st, 2017. I was upset that these two issues took so long to get fixed, however I did have a loaner car the whole time and nothing was charged to me in the end.
My car had been at Ford for five days before they even started to look at it. They blamed that it was right after Thanksgiving and they were backed up. On that fifth day, the technician who would be working on my car asked if I would come in and drive him around to show him the squeak. We drove around for 10 minutes with little luck of making the noise sound off. Of course, on this day, it had warmed up (about 60F) and the squeak went away. However, I had an audio recording of the noise on my phone that I showed to the technician and Service Manager.
After that day, they first began to fix the leak. Another individual in the shop (not my technician) had "made an adjustment" to the glass. They water tested it with air and soapy water and found that the leak stopped. They called me and told me that it was fixed and now they would start on the squeak.
Next, my technician began to find the squeak. The tech re-torqued all fasteners in the rear passenger side suspension with no luck of making the noise go away. He and the manager then spent two weeks trying to find the noise (making adjustments, driving, more adjustments, driving, etc...). Eventually they caught on that the squeak would stop when the rear passenger seat was down or if someone was sat in the seat. After this, they figured out that the noise was coming from the seat latch. They told me they adjustments to the latch and it stopped. Unfortunately, I forgot to ask the most important question of "What adjustments were made to the latch exactly?". But, 1000 miles later and the noise has in fact stopped.
BACK TO THE REAR GLASS!! I was called by the service manager after 3 weeks and he told me that the glass had began to leak again. Whooo. I get to drive a loaner car for longer. The manager said they would order a new rear glass from Ford and install it. Christmas time now. The glass took 4 days to get to the dealership. Then a third party was called to install the glass. While installing the glass, the company chipped the paint on the upper driver side crown/ridge of the window channel. I can't win. No worries though, I have rock chips on the front of the car that were bigger. Glass finally installed, and they even remembered to hook up the rear window defroster.
At the end of this month long adventure I gathered the technician, Shop Manager, and Service Manager to talk about exactly what had been done to the car so that everyone was on the same page and we could close this event out. I mainly did this because the communication between the dealership and me was not great. I had to call the dealership 95% of the time to get an update on my car.
Attached you will find photos of the leak that I took beforehand to show to the dealership (otherwise they probably would have doubted me and done nothing; it was hard to get it to leak since it was so small). Also attached is a sound clip of the noise that I showed the technician.