get a 5-speed.
a T-56 is such a hassle to swap into a 3.8 and it will make it feel, and actually will be, slower.
it will end up costing more than you most likely pay for the car.
the V6 T-5 gear ratios are:
1st: 3.35
2nd: 1.93
3rd: 1.29
4th: 1.00
5th: 0.73
and the Cobra t-56 to compare:
1st: 2.66
2nd: 1.78
3rd: 1.30
4th: 1.00
5th: .80
6th: .63
as you can see, the 6 speed has higher ratios for all 6 gears (other than 3rd and 4th, which are equal), and looking at the overdrive gear, .73 compared to .63, you will only gain slightly more MPG on the highway. but that's after wasting gas having to accelerate harder to get onto said highway