Well I'd say to change the timing tensioner, get a new Idle air control valve, get someone to time it right, possibly get a new throttle position sensor, reground your maf or get a new one while you're at it. try a new ecu of course do it one by one so you don't waste your time doing it all if it's only one thing, oh and I think what he meant by "muffler" is that maybe your muffler tip has something in it, or the exhaust is hitting the cross member, cause I've heard people play pranks with each other by putting a wrench in a persons muffler and it sounds like their knocking.
Also change the oil while you're at it