Any help is greatly appreciated with this.... I changed the latch cylinder and the hydraulic lines due to leaks, now my top will not finish the latching sequence and the rear qtr windows are not operating. I have checked the electrical connections in the windshield header and I have confirmed the hydraulic lines are not crossed.
The top gets to about an inch or so from the header and stops, then if I continue to press the top button for a few more seconds the latch will pull down a little more. The top worked perfectly before I changed out the latch cylinder and lines.

 

Hi - Since you got the car, you're not having much luck with the 1999 XK8's convertible top and you've newly installed hydraulic lines to the latch. As the roof moves, is the petcock valve, at the trunk pump, fully engaged? Have you put in new hydraulic fluid level when you closed the system after the repair? The hydraulic fluid would have needed to have been filled above the max line, on the pump, to fill the void in the new pumps. Is the level ok now? System is high pressure so air should bleed out okay if fluid is not old/contaminated.

Did you trying reversing the latch's piped connections (easily done at the hydraulic pump in the trunk) just to be sure they weren't "crossed."

Can you still disconnect the pump (petcock valve 3 1/2 complete 360deg turns) and manually close the roof using the Allen key. Then pressing the button, the quarter rear windows should go up. That'll check if all the microswitches in the hood mechanism are ok.

Check out this recent thread about Tuohy's similar problem with his convertible top.
https://www.jaguarforums.com/forum/
His final result was that old fluid had "gummed" up the works and needed cleaning out. The thread has a TSB fix PDF.

Good luck and let us know how you get on.

 

Good advice from David. I too think that you may have the pipes reversed or the system is gummed up with old fluid. Could even be the cause of the failure in the first place.

 

This could also be just a problem with the sequence. I had a similar problem when I disconnected the battery with the top in a weird position.

The car won't finish the sequence because it's getting weird readings about where in the sequence it is.

I had to manually close the top with the allen wrench, and this reset everything. After that my top worked fine.

 

Just had my own convertible top fiasco, as the top would not latch (latch was down) and the quarter windows were stuck down, and the top would not open either. Had all the lines replaced couple of years ago, by Marvin, after the infamous green shower. This was the first drive after winter storage.

Seems that use of the allen wrench while pressing the roof button seems to have somehow reset the operation, as it opened and then closed. Note of caution - the allen wrench will turn if left inserted and hit the roof liner; thankfully avoided that.