Grinding in the rear end of my car?

i have a trans am ws6 automatic pretty much stock except for my rebuilt tranny that has changed shift points, flowmaster exhaust, slp lid and nitto 555r drag radiails. with a professional driving and on a actual drag strip its suppose to run a 4.9 sec 0-60 and a 13.5 sec 1/4 mile stock. well i did the 0-60 test on black top and i got 5.5 sec but i only did it once. idk the 1/4 mile but i do know that my car is a bit slower on take off. i run a 0-100 in high 11 to low 12 sec. so im guessing my car will run the 1/4 mile in stock time if not a bit faster. well the thing is ive had a grinding in my rear end since i got it and im just gonna replace my stock 323 gears to 373. plus ill have to get a programmer to calibrate the speedometer and ima change it to where instaed of shifting at 6000rpm it will shift at 6500rpm hoping to get a bit more power. i also have 3 inch long tube stainless steel headers i want to put on but not sure if i will get to. but will i notice a difference with the different gears and the changee in shift points? if so how much would be your best guess. im wanting to know the performance difference cuz i alrede know gas mileage will be worse. and would the headers really help or just change to sound?