my 04 runs good, but gets a little slow bumpy idle sometimes if you sit at a light for a while. mine has a brand new head, and timing belt.
it has not jumped a tooth. mine has 144k, so i thought it was just getting old. it has thrown no codes. it gets killer mpg's. rolls down the hiway very well for a car with so many miles.
its an interference engine. if it jumped a tooth, i dont think it would run?
if it did run, it would run real bad i bet. 4 bangers dont like being out of time.
normally you will know when it aint right.
you might be on to something with the tcm re-flash though.