I appreciate your response on the matter of vw jetta vr6, replacing thermostat but was negligent on setting the timing and on this jetta the thermostat no is the answer to your question it wasn't running bad, he picked me up in the jetta to replace the thermostat only, it thermostat housing is located next to transmission above the starter no where near the serpentine pulleys. Well at least we got a laugh out of the crazy excuse they gave me by trying to get me to believe that I was responsible for this occurrence.
The timing can jump a tooth if the timing belt has not been replaced in 60,000 miles. Otherwise the crankshaft position sensor or camshaft position sensor may be at fault.
I would get the codes pulled. Any Advance Auto or Auto Zone will do this for free and you will have a direction as to which diagnostic path you will take. The codes give a desciption of the failed component. If the position snesors come up, it may not have jumped a tooth on the timing belt. If they don't and the timing belt is near the end of its service life, that is probably the faulty part causing the problem.