I've never been involved with anything like this before but is it possible one of the cables has a routing error? Beyond that I can only guess that one of the cylinders is the incorrect part for the XK.

 

Are you sure all the ends ( ball joints ) of the cylinders clicked in fully and didn't unseat ?

I congratulate on doing it all yourself though ! I wanted to do mine when my seals/ cylinder busted on my top a few months ago, but no one had put out a video yet and had a shop do it - would have been A LOT cheaper doing it myself !

g/l

 

All, thanks for the ideas, I checked for anything binding as well as the ball joints, all looks good. I have adjusted the 3 stops on the passenger side that I can locate and they have not moved the rear of the window noticeably closer to the cover.

Ill keep at it, any ideas or tips are always apprecaited. I have also reached out to my local dealer who has seen the car and asked them for any ideas. I am tempted to take it into them as well, though at this point they are not sure if this is something they can solve. They have reached out to Jag and some senior techs for assistance.

Thanks!

 

Where did you get the cylinders rebuilt? They may have some ideas on the cause and resolution as well.
I would not adjust any stops or the like until I knew for sure what is causing this.