How did you "disconnect" the siren? You may be able to by pass some or all of your problems if you disconnect fuse 9 under the hood. READ the identity card in the fuse box to be certain fuse#9 is correct. Seems each year could be a little different from the next as to which fuse does what.
The siren is located under the windshield cowl. When the cowl is removed the siren is in the center of the car. You should remove the siren from the car or replace it if you wish. You can drive the car fine without a siren. However, be advised the siren is the alert of the anti-theft system and from what you have mentioned in your #1 post it seems the anti-theft system may have a problem. That theft module is integrated into the air/vacuum pump which is located in the rear of the car under the truck. That air pump is what opens and locks doors as well as controls the flashing of the lights as well as the siren.
The first cause of your problems is leaking batteries inside the siren and then you may have a problem with water getting at the pump in the rear of the car.
Removing the cowl is not difficult, but you must get the wipers removed to lift the cowl and flip it forward.

PS Do not mess with that module under the dash until the others have been ruled out!!!

PPS the flashing lights are being set off by the anti-theft system. Try to rest the system by disconnecting the cars main battery for at least five minutes. After reconnecting the main battery the flashing light on the tow switch hopefully will stop flashing and thus your theft system is reset.