Going to need 4V COPS or the strap kit to make the 2V COPS work with the 4V. Also while its out he really should consider tearing the motor down and rebuilding it. There is no better time to do it then now when its out. The 2V computer should run it ok, enough to get it to a tuner at least or just flatbed it there. If there are 145k miles on that T-45... eh... have fun with that one... The 99s did get the carbon fiber blocker rings but still.
OR, if the mileage on his 2V is lower he could pull the heads, have them gone through and then bolt them on along with all the 4V specific stuff, rip apart the 99 motor and then sell the crank/teksid block to make some money back. If he's already a 5 spd not sure why he got another one. If he's auto he'd be better off keeping the auto IMO. He'll win way more drag races with it than with the 5 spd.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.