Honestly, the biggest issue I think you will have with this is the headers and the GT40P heads. With the spark plug angle on the P heads, the plug wires will burn up on the MN12 5.0 exhaust manifolds, as well as most headers. There do exist headers specifically to run the P heads on a Mustang, but they will at a minimum hit the steering shaft on your car, and may not even fit in the engine bay at all, since they are designed for a completely different platform. Also using the fox Mustang intake setup will make throttle cable setup difficult. My recommendation at this point would be to sell the P heads and get yourself some used aluminum heads like Trick Flow 170s or AFR 165s or something like that. Also choking this off with a stock intake is going to hurt you. The explorer GT40 intakes can be had pretty cheap, and also get the 94/95 adapter elbow, and it will work with a 5.0MN12 or SC throttle cable.
Didn't you use GT40p heads on your lemons car with the flanges cut off a donor manifold as spacers and extra long bolts? Did you end up having to do the steering shaft relocation or rig up something to move the spark plugs as well?