Either the arms or the pieces that are moved by the motor broke. The cracking noise is the pieces breaking. If your dealership is replacing it for free - definitely go that route. The part is only sold as a whole track which is outrageously expensive. I think that last time someone checked it was like $800. If you want to try to do it yourself...
1) Pop off the pillars that touch the headliner. They just pop out if you pull.
2) If you have an overhead console, pry the dome light out and take out the two torx screws that are holding it in place. Then the console just pulls out. There are two clips that hold it in.
3) Remove the rubber edge that goes around the sunroof opening on the inside of the car. It just pulls off.
4) Remove the visors. There is a plate that pops off (where it attaches to the roof), and then they are held in place by two screws.
5) Grab the edge of the headliner and pull down. It pops out easily. There is double sided tape near the sunroof, but it should pull off of that really easily.
6) Once the headliner is out, you can see how the sunroof is attached... The sunroof attaches to the track by two torx screws on the left and right sides. Take those out and remove the sunroof.
7) The track is held in place by about 12 bolts. Take them out and disconnect the motor wiring harness.
8) Take the track out so you can mess around with it indoors. That way you wont freeze!
Once the track is out, you should be able to see what broke. How it works is pretty self explanatory once you are looking at it. I don't know if you will be able to replace the parts though cause I couldn't really see how it could be taken apart. There are a few screws on the bottom side of it, but if you take them out it still doesn't come apart. There are rivets that hold it together. Unless you want to drill them out, I don't know if there is a way. Hopefully the scrapped cougar that you know of has a working sunroof so you can just get the whole track. Here is a link to how I fixed mine... I think that I am the only one to have successfully repaired their sunroof without actually replacing the track. I have only had it fixed for a few days though - so I can't say it will hold up for sure!
How I fixed my sunroof.
Also, you can sign up here to join the broken sunroof club... 123 and counting!
Broken sunroof club.
