Blinking while driving means the system sees a fault. If the light is on but not blinking while sitting still (but engine on), then the cycle did not complete the last time the top was put up and that is your fault.
If it does NOT stay on while stationary, the fault could be that the cycle didn't complete OR that the TCM sees something else it does not like (what, I do not know).

I don't remember where we were with this (because you started a new thread - that only makes helping you harder) but if the windows do not go down when you turn the "D" handle, either switch in the windshield frame is bad or the TCM is bad or the BCM is confused.

I'd try re-syncing the top if you have not done that. Start engine, put top down then up completely three times (including turning the hex-head bolt in the trunk).