Update on the top issue. I tested the latch switch by rolling the windows all the way up and then trying to lower the top. The windows did not go down when the top was moved into the first step of opening.

Not having the time to disassemble the windshield trim tonight, I decided to manually lower the top and then try to raise the top(with the engine running). Although the spoiler is up, it is in the fully extended position which allowed me to manually lower the top. The top was smooth in it's travel and everything stowed perfectly so I'm thinking I did not put anything in the wrong place when I replaced all of the cylinders.

Things are looking up(I thought) so now we try to raise the top, the tonneau unlatched and raised about 3 inches. Klaus had stated in one of the videos that he had to press the button 10 times to get the top to fully raise. With that thought in mind, I tried again with less luck this time but I could hear the pump running. I checked the tank level and it was nearly empty. with a sickening feeling in the pit of my stomach, we checked the void in the quarterpanel and lo and behold there was the fluid from the tank. I called Klaus to see if he had any ideas of what I may have done to cause this but it was after 4 PST so I left him a message and closed up the garage. I'll try to get back at it in a day or so.