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It could be a lot of things honestly. Best thing you can do IMO, is to finish off the tune up stuff you had planned. If you have something like a fouled out spark plug, or bad oxygen sensor your car is going to pull timing, and make you run rich to try to keep you safe and away from detonation.

It could be in the tune as well, or even a combo of things needing fixed, and a tune. Once you are at least fairly confident you have gone through and checked the plugs, wires, opti, ignition coil, oxygen sensors, fuel filter, and all the other stuff that could cause issues, and if you still are having issues, thats when I would give the tuning thing a shot.

It would be very helpfull if you had someone who can scan your car and plug in and do a diagnostic while driving it with a program like LT1 edit who is knowledgable enough to get all the sensor readings with your car to help pinpoint anything going bad or abnormal. This may help you narrow down what maintenance item(s) might be bad.