Hey what's up? Just my opinion but if your going to go through all the trouble of putting in a new engine, you might as well put a bigger one in. you say you have a 97 V6, well if your running a stock 5-speed T-5 tranny, you have the same transmition as the 94, 95 5.0's. you can keep the tranny for now saving you some money up front till you replace it and spend a little more on the engine. You can get a "new" ford rebuilt 5.0 with warrenty, from Mustang Part specialties (
www.stangparts.com) for $1750. They come complete from oil pan to lower intake so you really just need upper intake and front accessories. A 5.0 is not a real great engine but it is a lot better than a six as far as a starting point goes. anyway, just my 2cents.
Ron