Did you ever get the car fixed yet ?
I am going though the same thing with my car , My wife for some reason was trying to put up the window up...as I was closing the top , now it beep at me with the top up, I tried the re-sync process many time, without success, buzzed all the switches, all good , reset the D ring switch linkage, Then thinking, maybe with her pushing the window switch up and the same time ,That it took out the board in the modular , no change,
But now I'm locked out of the trunk as well , but I got the trunk open through the passenger side pleat light , on the long side ends of the light , there are push in tabs, with something like a butter knife , side it in between the plastic and the metal , push in and pull down on the plastic light frame . Then with a screw drive, push the white plunger/solenoid to the passenger side, I took the solenoid out and on the end of it, remove the ram end that stops the truck form opening ,( It un-snaps ) then remounted the solenoid , because the switches NO and NC are build into the unit to tell the Modular that the trunk is open or locked,
But if you have any more INFO on the reset , can you post it..
On the reset I did it like this... , with the car running, (1) I un-did the D ring ,(2) put the windows down,(3) took down the divider in the trunk (4) un-did the bow latch (5) put back up the divider (6) lifted bow (7) un-latched top compartment (8) Put top in slowly(9) re-latched compartment (10) put windows up... that's the full cycle I think ....