I got it fixed with the help of a member on the Facebook group. If anyone has this issue in the future the sensor with the short wires go down towards the bottom of the car. I had to take it apart again and reverse the sensors. I would also note that everything is working, however, the cylinder changing was more involved than I would have thought. Proceed slowly and I'd actually start with the bow cylinders, they were by far the easiest to remove. The main lift cylinders requires two people. You also need things to wedge the roof and Tanneau and bow up. I used a tennis racquet in a soft case as one to hold the Tanneau up (perfect fit) and wood with rags for the bow.

Also note fuses 5 and 6, 6 being most important to release hydraulic pressure if the top gets stuck.