I was wanting to know if I had to change the gears in my car or would it be alright to keep the stock gears?

Running off the headers would a x pipe into a 5" turn down be better or running pipe off the headers to 3" turn down pipes be better?

I have a 1999 Z28 with 96000 miles on it.Im putting a ms4 cam in and new springs, locks, retainers, pushrods, pro 5.0 shifter, spec stage2 clutch, hooker headers 1 7/8 3", ported ls6 oil pump, and ls2 timing chain. I already have ls6 manifold and ported throttle body.

 

If your car came as a manual, it already has 3.42 gears in it- adequate for a vehicle of this weight. You can go deeper if you want, advisable if you are trying to improve quarter-mile times, though your mileage may suffer a little. 3.73 or 4.10's are a common modification- be advised that if you start putting sticky tires on the back, and grabbing traction, your 7.5 inch rear end won't last very long. Usually cheaper to break traction than parts.
On the exhaust, depends on what final horsepower numbers you are shooting for. A 3" exhaust should support a little over 300 HP, if you have duals at 3 inches each, you have plenty of flow.

 

It's not a diesel truck so use 3'' pipes and mufflers.