1999 Pontiac Grand Am Well. My car is STILL having issue

My 99 Pontiac Grand AM (V6, 3.4) is really perplexing us. The car is misfiring when I accelerate and get to around 40 mph. We have changed the wires, spark plugs, fuel filter, had a professionl fuel cleaning done & had the ignition module tested. The EGR valve is only a year old. What are we not doing right? We have not changed the ignition coils yet. The car is running better since changing the fuel filter, but it still misfires. When we had the codes checked at Autozone, it comes back with random multiple misfires. I know this is going out on a crazy limb, but I have had problems with the security system for a long time. The system I have cuts fuel so the car can not be started. My secuirty light has been on for like 2 years now! Could this be the problem?