There are a lot of questions here.
What parts to turn a 99 V6 to a 347? There are probably a couple guys here that could answer that but I'm not one of them
, seriously, that is going to take a hell of a lot of work.
Nitrous (there are more people that make systems besides NOS), can be hard on your car, it just depends on how you use it (plus it will get real expensive filling a bottle up all the time).
If you want to fix up your V6 check out the V6 board, you'll get some good idea's over there. As far as the 347, post that one in both Modular and Windsor. Good Luck
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1995 Mustang GT