Check for hotmustang's VT Stage 1 cam install thread, it should be pretty much exactly the same as a PI cam swap, which I too will be doing here in the comming week(s).
When your car is in neutral, there is no load put on the engine, which means less fuel is used. When you put your car in gear, load is put on the engine, requiring much more fuel. Check your fuel pressure, you may not have enought fuel, or you might even have a clogged fuel filter, these all could cause hesitation. BTW, I have a 98 GT and I want to hook up PI cams, I think I know how to do it, but do you have a complete guide or walk-through for it, what tools did you have to use to make it easy.
Use the Anderson Tool. If used correctly it will make the cam install a breeze compared to dismantling the front of the engine. I used it and it works. Just be informed your low end torque may not be as strong but the mid-range to upper rpm power will be obvious with the PI cams.