The light is flashing? That usually means the PTCM has lost sync of what position the top is in. If you changed the cylinders, you were moving things around a lot - the PTCM has most likely lost track of where things are.

DO THIS:
Start the engine and put the top up and down completely (including the hex bolt lock) three times. See if that brings it back to life. Use the procedure exactly as described in the video below. Again, ENGINE RUNNING THE ENTIRE TIME.


If the above does not do it, then:
The sensors on the cylinders MUST be able to communicate cylinder movement to the PTCM - twice now, owners have had the same problem after cylinder replacement - and it was improper connection to a sensor on a cylinder.



One last thought:
You say that turning the D ring does not result in the windows going down. Think about how that works. You turn the D ring, the switch in the frame of windshield pulls a wire to ground, that tells the PTCM that the handle has been turned. The PTCM then tells the BCM to lower the windows. Now, what would interrupt this sequence?

A bad switch, sure, but you never fooled with that switch, so probably not. A blown fuse to the PTCM. An error on the CAN BUS from PTCM to BCM (not likely). A bad BCM (not likely).
Now, did you ever mess with the PTCM module in the driver's side wheel well? Probably not. I say it's a loss of sync. Le'ts hope I'm right, cause that is easy to fix, as I explained above.