if you found both door triggers, without diode isolating them, you may cause problems with the door circuit. possibly when armed, this will inadvertantly set your alarm off. in other vehicles it does different (more crazy stuff. ie if you open your drivers door, the car thinks you opened a passenger rear door)
programming a 3rd key is pretty easy. i would take the key and get it cut (anywhere they cut keys), that way you have a spare ignition key. the one that you want to use for remote start...don't get it cut.
their programming instructions should be similar to this:
*place spare key in universal bypass module. place antenna ring around ignition cylinder. connect wiring to remote start.
*put key #1 in the ignition, and turn the key forward (do not start vehicle) wait for (!) light to go off. remove key
*put key #2 in the ignition, turn key, wait for (!) to go off. remove key.
*activate the remote start.
since the ring of the universal bypass is around the ignition, it transfers the encoded chipped signal down to the key thats in the universal box. however, good placement of the antenna will be critical. if the key was cut and you could put it in your ignition, it would maybe be less time consuming?
regarding where you have it mounted/hanging. yes, i realize there are a lot of wires, and i know this was your first install... but for next time, plans things out better. the first place a theif is going to look to disable an alarm system is under the drivers side dash. so, hopefully all your wires are taped or loomed such that they don't give off any hints to where things may be found.
Certified MASTER Installer
one of 72 in the world...