Another update on the mystery top issue. For review, one evening I had the top down and it stopped working. It would not go up or down. After reading many posts here I checked the voltage at Pin 7 C1 on the PTCM. The voltage went to ground when I undid the D ring. The windows go down when the D ring is released as well. That eliminates the divider switch, the Top Release switch and the top open switch from the issue. Windows going down also seems to eliminate the CLP and the BCM as they are communicating. I swapped out the CLP with a known good unit and also the PTCM as well. Still inop. I was able to acquire a complete trunk lock and removed the micro switch. First I tested the switch to make sure it opened and closed, then I unplugged the existing switch and plugged this one in both the open and closed positions. Still inop.
So in my diagnosis I believe I've eliminated the:
Top Switch in the header
Top Open Switch on the right side of the TOP
Trunk Divider Switch
CLP
PTCM
Trunk lock
BCM
Can Bus
If any of these presumptions are incorrect, please advise.

This morning the car threw me a new curve ball! I had the roof down manually and put it up manually (always with the engine running). The light on the dash switch started flashing quickly and for the first 30-45 seconds of driving the car beeped quickly, then stopped. When I slowed down to under the 9 mph limit I got a slow flashing light and a slow beep until I sped up, then every time I went under 9mph it beeped until I finished my trip and shut the car off. This entire time the light on the switch flashed while driving. When I got back in the car a little bit later and started it, no light on the switch and no beeps!! What the heck!
When I got home, I shut the car off and then restarted it and released the D ring. Windows went down. When I hit the top switch I could hear the trunk lock but the roof did not move and after about 2-3 seconds holding the switch down I got a slow steady beep and a slow flashing light.
I seem to have a moving target and it really frustrating. Any direction would be extremely appreciated.

Would my next course of action be the check the voltage at the solenoids at the hydraulic pump?