I have a whole 99 motor in my 98 and the tune is stock down to swapping all the 96-98 stuff over like the coil packs vs going to COPs. Before you ask me a million questions though, I did not do the swap, the previous owner did. I can PM him and ask him if he did anything special. There is a TON of info online about doing the swap though, just use Google and read read read. More info than you can imagine.
2000 Mustang GT Steeda build #48. Bolt ons, suspension, Novi 2000.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.