2007 mustang aps997a w/dei 529t

Hello everyone.  I have a few questions that i know you guys can answer...Hopefully..lol

Okay...im installing a APS997A alarm and remote starting unit in my 2007 Ford Mustang.

It is a manual and I know everyone is going to say not to, but I am well versed with the dangers of having it installed and I have had a remote start installed on my manual vehicles for some time.  that being said, im really unsure of some of the connections to make.  The big ones im not sure about are the Clutch connection, as I know my clutch needs to be pushed in to start the car.  how do i bypass this for the remote start.  Also the emergency brake connection (I want it not to start if emergency brake isnt on).  if there is some sort of connection showing that im in gear, I would like to know about it so i can use it to disable remote start while in gear.  I have installed car alarms before...its just been a long time and i want to make sure it all goes in right the first time.

My next question is, can I use the window unit from DEI for this alarm system...i think its the 529t.  If so...how do i make the connections and how will i program it . 

If its possible to tell me the laymans way ie. red wire on alarm to blue wire on the car/529 unit i would appreciate it.

Thank you in advance for any assitance.