I modded my 3.8 at 350,000 miles (Green One). I also had it dyno tuned several times. It makes more HP than any other I have seen documented. It was strong when i got it, I took care of it very well ever since.
What I did was:
Change fluids, full PM. Differential fluid-Amsoil Severe Gear, changed it with cheap fluid first until i saw clear fluid come back out. Transmission fluid (T5 Manual) Mobil1 ATF, Motorcraft copper plugs (Or NGK), wires, coils. fuel filter, air filter, ect....
MODS: 3.73 Ford Racing gears, short throw shifter (MGW only), UD Pulleys, CAI, True dual exhaust, dyno tune.
The new 3.73 or 4.10 gears are the best bang for the buck.
'97 3.8L V6
1996 SVT Cobra White