`03 F-250 DSL 6spd & Matrix 3.5

Here's a couple questions for you folks...

I have installed my Clifford 3.5, and want to do the following.. Can anyone help me out?

A) I have hooked up the lock/unlock per DirectWire at the VSM module behind the radio. However, the truck has built-in keyless entry, which gives the truck the factory Dome Light Supervision. When I exit the vehicle and close the door, I currently have to use the keyless remote to lock the door to turn the domelight off, then use the 3.5 remote to arm the alarm. Otherwise, it states that a door is open because of the trigger voltage from the domelight. How can I fix this?

B) I have 2 DEI 530T module (Windows Up) for all 4 doors. What is going to be the easiest way to incoporate this with this alarm? I have looked at the triggers for the different zones, and they are either latched, delayed, constant or pulsed. Am I going to have to use one of the constant zone triggers, and just hold that zone on the alarm remote until the windows are up where I want them? I would like to be able to arm the alarm, and the windows go up when the vehicle is armed.

C) I know that remote starts are mostly for automatics. I was thinking of installing a "Cherry Switch" between the clutch pedal and the e-brake, so that when the vehicle is in nuetral, and the e-brake is on, the Cherry Switch will send the needed current to the clutch pedal wire, making it think it is engaged, and the truck will start. However, if the vehicle is in gear, AND/OR the e-brake is not set, the circuit is wide open, not allowing the remote start to work. Anyone have any wiring experience doing this?

Thanx for the help in advance!