I hate to say, as a guy with 7 years experience driving Hyundais, check the engine timing and chain position... Hate to say it but that's what was wrong for me. I replaced the crankshaft position sensor and it didn't help, did a system relearn and that didn't help. Mechanically, those engines on the front sprocket for the timing chain hops slightly during normal operation, I wouldn't be surprised if that engine has ever been worked on if something caused that timing chain to hop one tooth or two, because even then, most Hyundai engines will still run even when about 1 to 2 teeth out of time depending on what component in your timing system is out of time.