Compustar CS6900-AS in a 2004 Tundra Double Cab

First off, I've been researching and reading this forum for a few days/nights...You guys rock!! Tons of info and helpful tips for almost everything. I recently purchased a 2004 Tundra SR5 Double Cab, it did not come with a factory security system and fiddling with a key to unlock the truck while trying to load up a couple of attack Shih-tzus is a little bit of a pain, (I also have a 2002 Tundra SR5 Limited Access Cab and it had the factory security/keyless entry) I started looking at keyless entry and remote start systems.This past weekend I was discussing the differences and my girlfriend informed me she had purchased the CS6900-AS bundle for me as birthday present. So after spending too many hours reading and searching I have a few questions. Will I have to have the CM-600-AS "flashed" before it will function with the basic options? (remote start,lock/unlock, shock sensor,siren) Will it allow me to roll windows up or down from the remote? In the event I leave a window open and it starts raining. What other items might I need to perform this function? There is a tonneau(sp?) cover on the truck, I'd like to arm the tailgate to trigger the alarm, is there any special precautions for using a standard push pin trigger? I'm very comfortable doing this myself, have plenty of experience with stereo installs and such, so working around the airbag stuff is no issue...I have a DMM and know how to use it, all connections will be soldered, heat shrinked or crimped and sealed as needed. Any advice is appreciated. Thanks!!! If I can't find it myself, I ask...

no flash required.. it will work out of the box. (Assuming American truck with no immo) No to window roll up, unless you want to buy a DEI 529T As for the Tailgate, the hardest part will install the pin trigger / running the wire.. a mercury switch might be a better idea

Thanks Sir !! I just looked over the DEI module, looks like a 535T will be what I want to go with (2 actually since it's 4 door) that way I can roll them up or down either with or without the alarm set. As far as running a wire from the pin switch, I don't mind doing that, I'm more concerned with corrosion on the pin body preventing a trigger. I'm thinking I may be able to purchase the factory door switch(they are rubber surrounded) and mount it in a position that will have contact to open the circuit when the tailgate is closed. If I can't find it myself, I ask...