It obviously helped you off the line, but you just dont have enough power, 96mph is pretty low. Losing alittle mph after gears is normal. Gears dont give you more power, they just make your wheels spin faster, which you saw help out off the line, like I said you need more power to finish it off. When you can get over 100mph and a set of slicks or dr's, those gears will be helping. And dont spend too much time in thrid, you need to shift to fourth with 3.73's, shift into fourth like you shifted into second and third. I would set your timing to about 14 and shift at about 5400 use premium gas and thatll be the best you can do till you get some more power or lose weight, the car not you.
EDIT: I kept on reading, saw you got it running good.