Update on the top issue. Finally got a chance to get back to the Crossfire tonight. I had pinched the bottom O ring on the tonneau lift cylinder. I got that replaced with one of the spares that were left from the cylinder replacement. Filled the tank up, started the car and the top went right up. The top also went down with the switch also, no fault light flashing.

feeling pretty lucky, I decided to try and lower the spoiler and it worked just like it was supposed to. I'm gonna leave the trim panel off for a few days so I can keep an eye on the fluid level but everything is looking good for now.