So my car decided that the build was going a little too well. First of all the Mustang A/C line will not fit with the new jackshaft bracket and a new one will run about $185. I think we can make a new one with what we got. Second, when I installed the PCM in the car the anti-theft system was activated, so I have to figure out whats going on there. All in all the project is moving along, just very slow due to me being in school again. I received the short throw shifter from AmericanMuscle.com today and it looks pretty awesome. I will order the water to air intercooler kit fairly soon along with a universal piping kit. I have a list taped to the Stang's windshield and it is now less than one page long! Here are some of the latest pictures. 
Click HERE to view the intercooler kit. 
New Short Throw Shifter-
 
 New Short Throw Shifter-
New Short Throw Shifter-
-Engine in the Car

-Engine in the Car
-Supercharger Belts
 
 -TwEECer RT Installed on the PCM
Taken from http://mustangjames.blogspot.com/