Help with tuning/modding GT and Cobra

OK I am brand new at the mustang thing and so is my cousin. We both just got mustangs recently and are now ready to mod 'em.

He has a 96 5 spd. cobra and we need to know what gears to put in the rearend after we install the turbo. Seems like most people are saying 3.55's. Also we need a way to tune the computer after the mods are installed. How do you tune the computer for bigger injectors. We also have the same questions for my 03 5 spd. GT.

I have seen the flash tuners but do they allow you to control all of the needed parameters? His car has a return line and mine doesn't and is ran by a fuel pump driver module in the trunk.
 
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Of course I will take it to the dyno for the initial tune after the turbo install. I just don't want to have to take it to the dyno after every mod.

What gears are right for the Cobra w/ turbo?

How good is the Delta Force Tuner with the Special Forces Interface? A member from another forum said it was what we needed.