RANDOM/MULTIPLE MISFIRE CODE ON LS1 V8...HELP?

[HAHNSBIRD]

I have a 2001 Trans Am WS6 with the 5.7L V8 LS1 Automatic and I am contiually getting a flashing service engine code of "random multiple misfire" and a "6th cylinder misfire". You can definitely feel it missing or hesitating, its not real bad, but bad enough i am not driving it. I replaced all plugs with the new E3 plugs, new msd super conductor wires, new coil on 6, new fuel filter, new bosch o2 sensors, new k&n air filter, cleaned maf and other sensors and it has not changed. I clear the trouble code every time and it comes back on after a couple minutes of running the engine. I have a beefed up auto 4l60e and the engine has every bolt on possible along with long tube headers open y pipe and slp exhaust, along with a custom tuned computer. I only use Royal Purple Synthetic for all my fluids and I run 93 octane only always with an injector cleaner additive. Could it be a pushrod even though i have an automatic? An injector? Fuel pump? What? I love this car and it is my prize possesion! Please Help!

[HAHNSBIRD]

Its not the pcv,vacuum hose crack,fuel filter,maf sensor,iat,intake,o2 sensor,plug wires,exhaust,etc. I did notice that I got the E3 plugs from Summit Racing and they were #E362 and at my work (Oreillys) it calls for #E354 and there is a difference. So that may be it. Could it be the crank sensor? I have one in stock, but it is impossible to reach under the cowl!!! Also when i bought the car, my PCM was custom tuned and do not know where. I can reflash it back to stock at work. I might try that.
          Is it safe to drive an LS1 to a repair shop if the "SES" light is flashing? The code that shows up is random/multiple misfire P0300? One of the most random, pain in the ass codes. It runs well at idle but hesitates and misses upon acceleration and speed. What is the usual cause for this problem with this year/make/model?
     PLEASE SOMEONE HELP!!!!!