Give the OP a cigar for thinking to remove the glass before removing the sunroof. I wish I took the glass out first. It needs to be removed anyway to swap out the track parts I got from Sunroof Doctor.
I've had this thread bookmarked for many months while the replacement parts sat in the garage. I tackled this project this weekend and am just about done. I'm taking it slowly, but I wanted to thank the OP for sharing the process. With a three day weekend, and no hurry, I removed the seats and center console.
And I'll never use that stinkin' sunroof again. Probably. I don't want it breaking again. At least it's seated properly and won't cause any wind noise.
2009 Ford F150 SuperCrew FX4 5.4L w/Max Tow