Engine knock?

About 2 years ago, the car began sounding as though it had a rod knock that would develop during normal driving. But as soon as the check engine light would come on the knock would disappear. Then it began on start-up, with the same result as the check engine light came on. Upon pulling the engine down and checking the bearings and the crank with a micrometer, we found the bearings and the crank to be perfect to specs. We replaced all the bearings, buttoned up the engine, and began again. With the knock still present, we removed the air cleaner and found the knock to be coming from a backfire through the TBI. We checked for vacuum leaks and found none, then we went step by step through the ignition system till all components were replaced, still the same result. Earlier this year I gave up on finding the problem in the engine after checks in the valve train, timing gear, and all hard parts had been checked, cleared of fault or replaced. I then changed the ECM, no change. So I bought a replacement engine and upon fire up no knock. But within one week, the knockackfire was back. Can you give me any help here before I take 5 gallons of gas and a stick match to this car?