I posted this on an old thread thinking that maybe someone would see it that involved in the initial post, but it's been silent since I posted about 3 weeks ago. I had to replace some of the track pieces in the sunroof that were broken. When I put it all back together, I made sure to have the drill bits in the alignment holes before installing the motor. Put the assembly back up, and can't seem to get it to re-learn where the 'closed' position is. I've got the instructions that came with the kit from Sunroofdoctor, and I'm following them as far as I can tell. I took a video of both the instruction sheet and me trying it out. If anyone can tell me what exactly I'm doing wrong I'd greatly appreciate it. I can bump it up little by little to get it to the closed position, but I'd rather not put the headliner back up until it's fixed in case I have to take it back down. For those of you that have done it, you know it's a pain in the ass to remove and reinstall. Thanks again for the help guys!
Here's a video of me attempting the procedure with instructions: