I recently repaired by leaking slider and posted in the 1500 section, but wanted to post here since many likely don't frequent the 1500 section if the only have HD trucks.
I recently sealed my cracked, leaking rear slider. First, I took the headliner loose to about the middle of the cab. Then, I removed the spoiler and cleaned the roof and window frame with compressed air, water and then rubbing alcohol. I then applied AC Delco seam sealer along the top of the window frame all across. Let that sit for a day and then put 3M strip caulk on every bolt mounting surface and the 4 bolt holes on the ends. Once the spoiler was in place and nuts and bolts tightened, there was strip caulk sealing each side of every bolt and nut, as well as the 2 alignment pins. We've had some rain since and so far it is holding well. It wasn't a bad ordeal, but not something I want or will do on a regular basis. Too many other other choices of trucks to deal with this poor engineering, design and suppliers. Short of going to a glass company or body shop and having the fixed glass installed, this is good way to try to stop the leak yourself without going to the dealer and the aggravation of such. YMMV.