Well, problem has been solved. A-Train was 100% correct as usual. The problem was the MSD coil packs burning up and cracking, which was caused by the MSD box amplifying the signal from a bad EDIS Driver. Thus, I had to buy a new PCM and re-flash a new PCM. I have a little power loss from the MSD removal, but I will live with it, since I gained some power by having a dual exhaust system, so it was a trade off. The computer is still in its learning curve, I was getting a few misfires just after the install, but they only lasted a few seconds and then the computer corrected it. I put in some new gas and injector cleaner and it seems to be okay now. I gather that I had some deposits in the #5 & #7 Chamber since there was no firing for a while, so I am breaking up the garbage.
Also, Leland, thanks for the advice on the MSD crap. AED disconnected all of it and I am sending it back to MSD, since it is 5 months old and has a 1 year warranty. The stuff is crap.
AED 9 PSI Supercharger, .30 over Forged Block with Manley H-Beam Rods & Pistons, Innovative West 10% Overdrive Crank Pulley, Thump RRR Tensioner Pulley, Cobra Crankshaft, BPE Racing Stage 2 Ported & Polished Heads, Crower Direct Replacement Cams, 70MM Throttle Body, MAC Cold Air Intake, 80 MM L-MAF, 38Lbs Injectors, JBA Ceramic Coated Headers, Metal Matrix Drive Shaft, Kevlar Clutch & Kolene Reaction Plate Transmission, True 2.5" Dual Magnaflow Exhaust (Cats & Mufflers), Griffin 1 1/4" Radiator, B&M Racing Trans Cooler, Hughes 2750 Stall Torque Converter, 3.73:1 Gears with Traction Lock Differential, Trans-Go Kit, Superchips Custom Tune for Supercharger, 17" SVT Wheels, Kenny Brown Suspension Enhancers & Eibrach Lowering Kit.