@RobbiZ4 - Great news (with one small problem left)! I bought the 540320 tool to unlock the rear roof and it worked great. Super easy to use. If anyone needs it you can purchase it from Turner Motorsports:
https://www.turnermotorsport.com/p-31655963-tools/
I then took a 12V battery and touched the two wires to the large lines on the roof cowl locking motor and it unlocked the front cowl. With the pneumatic pump valves open again I was able to manually lift the two roof sections up and take the tops off to get to the wires again.
After getting the roof open again, I undid all of the connections on my wires and soldered them up with shrink tubing that had built in adhesive (great stuff for keeping moisture out). All of the errors cleared up. I then removed the kinetic boxes in the trunk (boot) and replaced the two switches (one on each side) and soldered those lines back in too. I then soldered the final lines to fresh connections into the 26 pin connector for the CTM.
Unfortunately the open and close buttons in the center console still don't do anything. So, following your recommendations, I put a back pin into pins 13 and 14 on the 41 pin connector (which are the ground lines from the open and close buttons). I tried to see if there was any voltage being registered with the car on but 0V DC was all I got (I thought maybe it would be 12V and then 0V when triggered). I also tried to measure Ohms and it stayed Open (Infinity) no matter what I did with the buttons. Finally, I ran the line from each pin (one at a time) to ground on the car and as soon as I did that the roof started moving. I was able to get it to close fully and the red flashing light went off and I could move the windows up and down. I then got it to go fully open (with roof package in the boot) and windows also operated when it was done with no lights flashing. I did this 3 times in a row and it worked perfectly each time.
So...I'm super close. I just don't understand why the buttons aren't triggering the Top to go up or down.
I'd love any suggestions you might have for next steps. My thinking is to pop the center console open and pull the button switches out and see if I get a closed circuit between the button and the 41 pin lines on 13&14 in the CTM. If I don't then there's a breakdown in wiring between the center console and the CTM.
One other oddity is somewhere along the way of fixing the roof my passenger side seat (right side of the car if facing the engine from the seat), I started getting errors related to the passenger restraint safety system. Is that somehow related to the open/close buttons?
Thanks for all your help! I'm so close to being done!!!