cappak,

What ZERACER said. I just went through replacing all the hydraulics and tonneau cover lock. The top could be out of sync. You owe it to yourself to get familiar with the manual raise and lower of the top. Do you have the factory wrench which allows you to do this? If not you need a thin 10mm open end wrench and a 6mm hex wrench. Car must be running to minimize electrical load on all the modules. Do a complete lowering and raising of the top 3.times. This complete includes locking down the top bow to the tonneau cover from inside the trunk using that hex key when you raise it up, top up. After 3 complete cycles of down and up, then try pushing the button to lower the top. The PTCM is probably OK. You said the only reason the top was inoperative was leaky cylinders. There's been no evidence of water in the pump well, driver's side rear, right?

One other thing to mention 'cause it happened to me is the bow lock assy needed to be adjusted. That part has a mounting bracket that is slotted. My top would not complete it's cycle until I loosened the 3 bolts and raised up the lock mechanism then tightening her down.

Let us know if this helps.

Regards,