99FormulaWs6

Over the weekend, we swapped an LS6 intake and pacesetter headers on a '99 WS6 and everything went smooth until we started it up, and it started knocking, it suddenly stopped, and then restarted. What could this be? It sounds like it's in the valve train, but we didn't touch anything in there. I'm ready to puke. The only thing I can figure is during the swap, a sliver(the size of a pencil lead) of plastic fell into one of the ports and is beating around in there. Is that possible?