ZX2 running rough

2002 Ford ZX2. Pushing 90,000 miles. Timing belt and related parts were just replaced a few months ago.

Past few days the car has been running rough when the engine is warm. The first time it happened. The Service Engine Soon light would flash whenever it was jerking. Took it to the garage after work(engine was cool then). Ran fine and no errors came up when it was attached to the machine.
Filled gas tank and added fuel injection cleaner.
Ran perfectly fine the next day. No issue. The car sat over the weekend and was driven for some distance that sunday night. Again it began to run rough(jerking) and the check engine light came on and remained on.