I dont know how you missed it, but you must have the engine running to re-sync the top, without the system powered up, the TCM is not "awake" to learn anything.

Now, as to the window, I recommend you replace the top with a BAS top from the UK. I reglued my window four times in four years and will never bother with it again, other than for an emergency repair.

But some people have good experiences with re-gluing a top, here is a video by a forum member, Greg who seems to have the patience to do this right, I don't:

https://www.youtube.com/watch?v=JgN2...ature=youtu.be