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Yes, you can use the acc output of the alarm(red/white wire), but if i remember right, you will prob have to hold the button down to keep the windows rolling up(its usually run off of the orange ground when armed wire, which keeps a constant ground)I've never realy done it this way before, so not sure on that one, until its actually hooked up. If you do it this way, all you have to do is reprogram your transmitter for the RS feature. Open your driver door, and turn the key to the run position, and get at your valet button. Push and release the valet button 2 times, then press and hold on the 3rd.The red LED should blink 2 times, repeating itself. Press the auxillariy button once and release. Now advance the valet button 1 more time,(release-press-release,press and hold), LED should blink 3 times. Press the lock and ulock buttons at the same time, then release. Release the valet button, and turn the key off. Wait 10 seconds, then try it out. The lock/unlock buttons pressed together should start the car. Aux is now set to channel 2(red/white output wire). If you install the window module, you will have to take note and not wire it like the install manual says..instead of using the alarm's orange wire for roll up, you will connect it to the red/white, and window roll down wont be on the red/white, it will go to the violet/black.
You will not be able to roll the windows down by remote, unless you use wire it like above and use another output channel. It's supposed to be wired so that the orange ground when armed wire is activated(lock, and remote start-if you dont want to do it on RS, turn off anti-grind)it rolls the windows up, and window roll down is controlled by the channel 2 red/white wire. But you are in luck, the 790 has one more output channel, the violet/black wire. This can be used to roll the windows down. This is channel 4 output wire. Hopefully you can see this, but this is the manual for your system:
http://www.directechs.com/guides/manuals/ig/viper/N554V.pdf
This will also tell you how to program the transmitters and also all the options/features you want.
As for doing the sunroof, you MUST use another module to do that, or else it will mess with the window module. The window module works by sensing the current draw through the window circuit. When the window is fully up or down, the window motors dont move anymore, and the current draw goes way up. The window module senses this current, and shuts down power to the windows. If you tied the sunroof into this, the roof would either not fully close, or not fully open, just because the time it takes to do that, compared to the time it takes the door windows(it may sense the sunroof fully closed, then shut down power while one of your windows is still not fully open or closed). The window roll up module can control 2 windows only. I believe they make a module just for sunroofs also, and all you will have to do is tap off of your red/white and violet/black wires to control that, just like the window module.
The window module also gives you one touch up and down features on your stock switches, which is really nice to have. The module interfaces with your current window switch circuits, and with that hooked up, all your stock switches do is control the window module, instead of directly controlling your windows. 
13.5 @108 MPH-2.2 60ft(stupid FWD!)
S16G @ 18 PSI/FMIC/Running on MegaSquirt II (Now with sequential
fuel injection)
My webpage: http://eclipsed4evr.home.comcast.net
-1998 Mitsubishi Eclipse RS-T- "Toy"
-1992 Plymouth Laser Turbo AWD(SOLD)
-2000 Honda CR-V(daily)
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I have my remote start on my aux channel rite now. So what would I move the remote start to? Also would I have to buy another module to do the sunroof or can I just run the positive and negative wires from the sunroof to the module so it operates with the same module. 
