Roof unsecure warning light

Try the simple stuff first. Is the roof fully locking into place when up and down? Sometimes a faulty or dirty roof switch can trigger the theft light as the system thinks the roof isn't locked.

Yes, I would lean toward a stuck drivers door latch. Your door open switch is located in the latch itself and the ding is a reminder your key is in the ignition so you don't lock them in the vehicle when you lock the door. even though your door is shut, the truck still thinks it is open. sometimes spraying the latch with some WD-40 will get it freed up and working again, but a new latch might be in your future.

You need to have the VW dealer or a well equipped VW savvy repair shop scan the body control module (or whatever VW calls it) and see what codes return, it is likely the problem, but hold on you can't jut pop one in it must be programmed for your car.

for one thing, you have a vacuum leak. this is causing the locks and engine shut down issue. start by disconnecting the vacuum tube that goes from the engine compartment through the firewall to the inside of the car (drivers side near brake booster/reservoir). disconnect and cap the engine side and tape to make an airtight seal. now, if the engine shuts down with the key, the leak is inside the car somewhere. to isolate inside the car, disconnect vacuum at each door 1 at a time and see if the other locks work. If you get this far, remember, you have to hook up the vacuum tube you capped in the engine compartment.

Go sit in your truck and close all the doors. Light stays on right? Put your key in the ignition. Does the chime start going off when you put the key in? If so, door switch or the GEM thinks a door is open.

To find out which door... Leave the key in the ingntion. Turn to the on position. Even with doors closed, chime sounds once after a few seconds and door ajar light comes on and stays on right? Open each door one by one. The chime should sound each time you open a door. When you find the door that doesn't make the chime sound when you open it, that is the problem. (Don't forget to try the rear hatch and the hatch glass also!) To determine if the switch is bad or if the GEM is having a problem thinking the door is open, just unplug the suspected switch, close all the doors, and see if the problem stops. (don't forget to wait a second to give the lights time to go off) If unplugging the switch solves it, the replace it. If it doesn't, Ford can check your GEM to see if it is the problem.

I hope this helps

Insert the ignition key and turn from position II (Ignition) to position 0 (off)
and back four times within three seconds. Remove the ignition key.
The locking control system is now in "learn mode" for the next 20 seconds the
red warning system LED stays on continuously to indicate this.
During the 20 seconds press one of the transmitter buttons. The remotes signal and
code number is learned by the locking module and is indicated by flashing the
warning system LED.
Wait until learn mode times out (20 seconds) or switch the ignition back to ON.

switches are in the latch and you will have to start by turning the ignition key to on and then open and close each door. when you get to the door that doesn't make a chime sound when opened or closed. that is the door with the latch problem. you will need to replace the switch for that latch

refer to the owners manual, for instructions to put down roof by hand, they are not easy to follow, however, the manual key they refer to is in the fuse panel, the 1st lock to undo is in the middle section of the back seat, next the lock for the front section push down roof and lock in place. the warning light at this point will still be flashing, and the display saying roof unsecure. the bit everyone seems to forget is to go back to the middle back seat lock and relock, once that is done, display clears, and both roof and boot should work. i have no idea why this fault occured just hoping its doesn't too often. suggest also you always have engine on when operating roof. hope you find this usefull.

have you tried starting the car ,if not lock the car, open with key manually and try and start

Check the wires that are going to the brake pad sensors.Some shops will install pads that don't have the sensor connections on them, causing this light to stay lit.