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I have a 99’ vw jetta 2.0. I need to pass the emissons test. I took it to the dealer their hand held device said mis-fire on 1 so, the spark plugs and the coil pack was replaced and the check engine light is still on. I do have a performance cam shaft in. Does the ecu/cpu just needs to be reprogram?

 That CEL (check engine light) is just a kid in class waving her hand trying to get you attention because she has the answer. You need to have the codes read. Some places will read them for FREE. Try Autozone or Advanced Auto Parts. Get the exact code (like P0123) not just their translation into English and post it back here. 

Sometimes the engine needs a few cycles before a corrected error resets.

What has been done besides the plugs & pack? Are those standard wires and was the wire replaced?

You can swap the #1 injector with another one to see if the misfire moves. The injectors also have resistance specs that can be checked.

You may want to check compression, especially since you messed with the cam.

There’s a lot that is unknown about this situation; how long this camshaft has been in there, was it there the last time the inspection was due, the camshaft profile, details about the valve lifters/lash, and the state you live in are some of those unknowns.

With a performance problem one should always check the compression first to weed out any possibility of a mechanical fault. (say an inadvertently bent valve due to a broken timing belt, a timing belt that not installed correctly after a cam change, etc.)

With some camshafts the engine may not pass emissions anyway, misfire or not.