[JL8Jeff]

I don't remember the specifics on the LS1 setup but the crank position sensor could be getting bad readings. Does the engine sound any different when the check engine light starts to flash before it goes on solid? When it's flashing is when the actual "misfire" is occuring and it will often show a specific cylinder code at that point in time. My old 96 SS would do it all the time and the car ran perfectly fine. I replaced plugs, wires, coil, ignition module and it still would happen randomly with no affect on the way the car ran. But starting with the basics like plugs and wires is a good idea.