I installed my own remote start/alarm, never having done one before, and it worked out great. I used this guide to install it, and it has all the wiring colours, and where they are located and cross referenced it with the ford wiring shop manual I have.
Just remember to test every wire with a multimeter before you hook it up.
For the transponder I used the DEI 1100F but I think it's discontinued but you should be able to find a comparable model. It only sends the code to the receiver when the remote start is active, and you don't have to leave your other key in your car. I believe it was only 4 wires that had to be spliced in by the ignition, but I think I had to look in the shop manual to figure out where they went and I don't have it handy right now.