2000 Honda Civic Car hesitating

Other Category problem
2000 Honda Civic Two Wheel Drive Manual 103000 miles

My 2000 Honda Civic Si just had a tune up with the plugs, cap, rotor, wires, fluids being replaced. When I first start the car and running cold it has a bit or restriction with the acceleration. After warmed up, the car runs better. When I reach speeds of over 60 mph or nearing 5000 rpm, my car hesitates and I have to wait a few seconds for it to power through to it's typical performance. My car is supercharged and I have not had this problem before in the 7 years I have owned it with the charger on it also. I have a fuel pressure regulator and valve and the pressure is fine, I also tested for vacuum leaks and found none. Not sure if it is the mass air flow sensor or something having to deal with the exhaust system. I have a 2.5" performance catback exhaust system. Any ideas would help as I feel that I am losing performance power.