A water damaged CLP/SSM will disable the top, sure. But generally speaking, you will have lock issues as well.

But the way you describe this, it's as if everything was fine until you changed the cylinders. In that case, I believe you have a sensor somewhere on a cylinder that is reporting a conflicting position.
And since you tried to re-sync and it did not work, well, if the sensors are set up wrong, re-syncing wont work as the sensors are reporting erroneous information to the PTCM.

Rick Dunmeyer in PA has a STAR emulator that will read what the sensors are telling the PTCM. He can find an issue with a top in a few minutes when it's a bad sensor. I don't know of anyone in the southeast USA that has one.