It's not as simple as the dealer loading 99 program into earlier computer. Different hardware, different software, different wiring. The only change in the tune that would be 100% necessary is the larger fuel injectors. I would either have VMP make you a mail order chip, or buy a Sniper Delta Force tuner for $360 and do it yourself. The Sniper is very user friendly and you can do a lot with it.
Myself, I just dropped a 05 4.2L long block in my 94 and I'm buttoning it back up this weekend. I will be fixing my tune with a TwEECer and Binary Editor, then burning it with a Moates burner and Moates chip. I went this route because I already ahd the TwEECer for my fox, and I plan to use it for other cars later.
1990 GT 5.0 - H/C/I
2003 GT - bolt-ons, 87 octane, 252/298 rw