OK, the last thing to do was to wire the brain up - all the sub sections of the installation have already been completed, leaving me honestly not much left to do. The fact that this is a work truck (not many options) AND a very basic vechicle made it easy to make this a very clean install.
The first thing to do was to find a mounting location for the brain. When I first pulled the brain out and realized how bit it was I knew finding a location for it was going to be hard. Under the dash of the F150 there is basically only open space. I tried a few nooks and crannies but wasn't happy with any of the locations under the dash. I then proceeded to remove the cluster trim and luckily found a PERFECT spot right behind the cluster. The brain fit perfect and it allowed me to run my ignition / OEM security wires down the passenger side of the column cleaning and then route my ground/door pin/parking light/brake/actuator wires down the drivers side of the column. The only drawback was that it was impossible to actually work behind the cluster, so the install is only as clean as my prep (which is acceptable in this case). It's really hard to "see" the brain in the picture because it is a tight fit and there is a large OEM wiring harness running over top of it:

Like I said, I ran all the "little" wires down the passenger side. I was able to grab the parking light wire right at the switch - right now I regret not taping that last section of wire!:

That loom then continues down to the lower kick area where my door pins, ground, and brake weres were located. I took an extra minute to trace out the brake wire because I didn't want to tap it at the brake as it would have been difficult to make that connection look OEM. The little extra work paid off and it was right in the kick panel with the door pins:

I had to diode isolate the door pins and my little trick there is to solder a loop of wire on to both ends of the diode on the bench, then cut the loop and install the diodes as needed. This eliminates having to wrap the diode around the OEM wires and makes it a bit easier to hide:

Here are the connections after being soldered (the ground is at the very bottom, soldered to an OEM ground wire):
With the wires connected I loomed and taped them and they disapeared in to the OEM wiring! (please ignore the actuator wires, I did them last):

I ran the antenna up the drivers A pillar and tucked it under the headliner. I ended up mounting it right behind the mirror, behind some tint - I know this isn't best for reception, but with a 1 mile range or whatever I wasn't too concerned (and I now have too much range how it is!):

I then moved to the ignition wires. This truck only has one ignition, one accessory, and one starter so it was cake. The biggest issue was soldering all the power wires to the main power feed (there were three heavy gauge power wires and the power wire for the alarm). In order to make the starter wire splice appear more OEM like I ran the DEI starter wire a little past the splice and bent it back to connect to the wire - this eliminated an awkward splice in a "busy" area that would have been hard to conceal:

After I got all those hooked up I was ready to test the system. Everything worked great EXCEPT it would only remote start if I had the key in the ignition. This was an easy one, my security bypass hadn't shown up yet so I was done messing with it for a few days.
Once the security bypass showed up I hooked it up as directed (right to the plug on the ignition key cylinder). I programmed it as directed and it worked the first time!

Although it worked, I didn't feel that that was the best way to hook it up. I traced all three necesarry wires from the plug down to the main ignition harness (where my other splices were) and I then soldered all the connections down at the base of the column. I loomed and taped and was ready to put the truck back together!

At this point, looking up under the dash you can't see a thing. I would be surprised if even a Ford tech would notice anything out of the ordinary!
I still had one thing left to do though, and thats tie in all the actuators. I routed them up through the dash and to where the brain is. I replaced the door lock harness that came with the alarm with a 451M (door lock relay module) I had in my toolbox. I then hooked the door actuators directly to the 451M and tested them out - they worked perfect! I then thought about how I wanted the tailgate actuator to work - I knew I wanted it to lock EVERY time I armed the truck so I hooked the lock wire up to the 451M lock output. My original plan was to use an AUX channel to unlock the tailgate but I decided, in the end, to hook it up to the priority door unlock output. After playing with it this was byfar the better way to go - it is very OEM like and I didn't burn up an AUX channel on an unlock task. I didn't take any pictures of the relays, but they are all tucked behind the cluster with the brain and the security bypass - completely out of sight and very difficult for a thief to get to.
The only things I have left to do at this point, besides finish putting the truck together is to mount a door lock switch I purchased from Spal and to seal my grommets I poked. This switch will allow me to electronically lock and unlock the doors from inside the truck and I'll have to buy some sort of silicon sealant to seal my two grommets (the second one was in the floor board for the tailgate actuator).
In the end, I'm very pleased with the system and the installation. I wish I would have ran a spare wire back to the tailgate so that I could add a switch to the gate and I wish I would have used a better hood pin, but both of those are easy fixes if I ever feel the need to upgrade.
I hope that this documentation will allow people to see the amount of work that goes in to a typical remote start / alarm system. If you are reading this and have never done a remote start / alarm PLEASE note that this truck was about as basic as you get - there was nothing difficult or out of the ordinary on it. Many, many, many cars are much much much more compliclated then this! Also, remember to test EVERY wire with a volt meter (not a test light). If you aren't sure how to test for the correct wire seek professional help - hooking things up wrong is a quick way to damage sensitive electronics. And, besides the fact there are usually multiple wires of the same color in the bigger bundles I have came across installation charts that were flat out wrong - verifying the connected BEFORE hand is the only way to catch those mistakes!
Kevin Pierson