white99ta!!

Hey guys, I recently replaced my transmission and put a super street fighter 3600 stall converter and as soon as I was done it started throwing a random/ multiple cyl. Misfire. Any ideas on what would cause this? I replaced the plugs and plug wires but the plugs were fine. They had a brownish tint to the indicating properly working plugs. I read somewhere that the higher stall could cause this. Could that be the problem. The car runs great and has no loss of power. Im waiting on getting my diablo predator back from my tuner in hope that the new tune. Any help would be appreciated.