Okay here's a rundown of all the problems I ran into...
A) Fuel pressure loss- The
BBK SSI intake was to blame. The tube inbetween the fuel rails was leaking.
B) Vacuum Leak- We had accidentally pulled the PCV valve out.
C) Spark plugs- The GT40X heads take 3924 (I think) Autolites.
D) Valve train- The rockers must be shimmed exactly as shown here:
http://www.stangnet.com/mustang-forums/785764-cam-timing-question.html#post7909781
E) Timing- The black "reluctor" has to be pointed at 12:00. The rotor should be just behind it. The number 1 plug on the cap must be over the rotor or just after. That plug actually sits just over the black magnetic pickup (reluctor I think).
F) Fuel in the Oil- After many attempted starts the unburned fuel was just pooling inside the combustion chamber and you could tell from the plugs. Some were black and some were clean but they were all drenched. It was obviously washing out the cylinders.