I bought a 2001 that had a dead engine and had been sitting for a couple of years. I had a low miles (100k) engine that came out of a car damaged by the Joplin Mo. tornado. Swapped the engines and it ran great for the first mile but once it warmed up it would belch, fart, miss and pop back thru the intake. It seems to always start running bad as soon as it warms up. We drained the old gas and that did help some but not completely. No check engine light or codes are set

 

Fuel pump?

 

timing belt skipped a tooth

 

why would you say that the timing belt "skipped a tooth"? We did install a new timing belt before installing the motor. If this is a diagnosis why does it only show up when the temperature comes up to operating temp?

 

Well thats also a possibility.

Engine when cold will run in open loop which is a rich condition and computer doesn't pull timing till warm at which point it will run in closed loop and pull timing.

Some cases I have seen fuel pumps run progressively worse the longer they run the more fuel pressure they lose.

I guess a good place to start is to get a fuel pressure gauge then go from there.

Remember to always try to keep things simple, an engine is just a giant vaccum pump. It needs air fuel and spark to run, and the correct amount of airflow and properly timed fuel and spark to run right.