missing w/ msd ignition

I have a 89 mustang GT w/ the stock 302 block. It has an intake, a bigger throttle body and mass air meter, heads, a fms cam, bigger fuel pump, headers, and a battery relocation kit which are just the major mods. I installed a 6al box, blaster coil, adjustable rev limiter, and a msd harness. After intalling all of that my car misses under load anywhere from 1/4 to wot while I am driving down the road but it is fine when just revving it up. I am running a stock distributor, msd cap + rotor, ford racing 9mm wires, motorcraft plugs gaped at .060 and the timing is set at 12 degrees advanced. The box is mounted on the drivers side fender where the battery used to sit. It is grounded directly to the 4 gauge wire coming from the battery and the power wire is coming from the starter solenoid. I have rerouted my spark plug wires with a diagram found on a 94 ford truck which seemed to have help reduce the missing and I also changed the sparkplugs from autolites that were gaped at .052 and they looked good. But I can disconnect the box and the car runs fine. Other things I have tried is turning up the fuel pressure up to 49 lbs., unplugging the rev limiter, and disconnecting the battery for 30 mins to erase the computers memory. Also it seems not to miss as much when the car is warm. Any help is appreciated thanks, Bolinger