if you have a 94-98 v6 and put the same things on it that I have on my 04 stock v6 (my heads and my split port intake manifold and my cam) you would have almost the same horsepower within 10 horses [I say that because of wear and tear on the engine]... However if you leave your cam on and just put the intake and heads on, you may have a little more horsepower than I do. [reason being is that the cam on the 94-98 is a little more aggressive.]
If you go to this website you will see that they say something a long the lines of what I just said and you will see how much the swap actually cost. http://rpm-mustangs.com/cart/home.php?cat=322
For those that are like me, its only $720 USD... However, the actual horsepower that reaches the ground in the 99-04 especially the 3.9 liter v6's of 2004 are roughly about 3 to 5 hp more and about 5 lb of torque more. This is because the auto tranny is a little more efficient and the engine doesn't loose as much horsepower to thermal energy (heat) as does the older 3.8s from 94-01... I think in 02 they came out with the v6 having 193 hp.