Most likely due to bad spark plug wires... I've had these go bad several times over the life of the car. Also be sure to use the correct dual-ground spark plugs.
There are several things that can cause a clanging noise on your 2004 Toyota. A loose exhaust pipe is the most common cause.
Possibly the sway bar bushings?
A bad cdi, will cause no spark if its completely bad, but if its going bad can cause misfires, random stalling and rough running, like alot of backfiring and stuff.
Spark plug. Plug wire, or coil
check for tune-up. chack mass air flow meter.
The distributor cap of an ignition system is one possible cause of many for misfires. Other possible sources to investigate are the distributors cap and gears. The flow chart of diagnosing misfires also include the coil, capacitor (if applicable), ignition wires and the spark plugs.
It can cause a rough idle and random misfires because the engine will be off balance. If the flywheels happens to stop with the missing teeth (tooth) in the starting position, the the engine will not even crank.
There are pages and pages of things that can cause a check engine light. You need to have it checked with a scantool. Then the code can be diagnosed and repaired.
incorrect engine timing so that it misfires
I'd use Toyota plug wires to replace the old ones. I used generic wires from auto parts store and within 10,000 miles had to take 4runner in for engine running rough. The cause was ...... faulty plug wires. Replace one wire at a time and put new plug wire where the old one came from.
Cross-threaded spark plug.
No, but bad spark plugs or plug wires sure can.