Everything has almost been replaced,still check engine light

Less than 2000 miles ago i had a cracked
head on my 88 inline 6. At that time along
with the head, the water pump, clutch fan,
exhast system from the catlicconverter
back, and radiator and thermstat were
replaced.  With all that work, i still had a
check engine light come maybe half the
time. I was told that an oxgen sensor may
have gotten wet, and that would causr the
check engine light to come on, now that is
teplaced, still have the partime emgine light,
while its on, it run a little ruff and sucks gas!
Whats is left that would cause this.