Hi Greg, reading your posts again, it's an interesting fact that you're able to engage the gears with your diagnostic tool but not with the paddles. That alone eliminates quite many root causes and it really looks like your clutch can't engage/disengage. Can you please check the entire clutch hydraulic lines and make sure there are no leaks, including at the bleed block and nipple, or anything else that would be suspicious on the hydraulic pipes?
Stef, you and my local F12 friend Sandro had similar ideas. I have checked and found out that I am the root cause of my problems as usual.
Apparently, when taking off the engine bay covers, I must have hit the line and disengaged it (picture of pipe attached). I plugged it back in, and everything is working well.
Possibly before it was only partially off and so I didn't see it, but also I was more focused on looking for electrical connectors and was ignorant of this systems pipes and connections. Feel a bit foolish after finding such an easy solution.
So, it wasn't electronics, it was just a simple disconnected pipe that lead to my many week search but I learned a lot about the car in the mean time.
Ready to drive: Thanks to everyone for their help in resolving this problem!