It should fit but you will have to convert all the accessories to the 2000 GT style. You will have to switch over the tensioner from the 2000, probably use the short neck water pump (if that was on the 2000) and I think there is an extra idler pulley on the newer timing covers. To take it off you will have to take off the belt and all the accessories including the harmonic balancer. There are a couple of bolts on the valve covers and the oil pan that will have to be removed. Also the power steering pump and the AC compressor will have to be unbolted. It's not a hard job but just take your time. Give yourself a few hours or even a whole day just so you don't make any mistakes. BTW, why don't you just use a 96-98 timing cover...??
Don't forget that the 1999-2000 Mustang used a Windsor block. The Windsor block uses 10mm diameter bolts on the timing cover. The Romeo block uses 8 mm bolts. Not sure if the difference matters but its too early in the morning to think about it.
Will the difference in belt routing interfer with the coil packs?
Good point wmburns, the belt just might run into the coil pack on the passenger side. If that is so, then he won't be able to use the newer timing cover. BTW, I didn't know the 99-00 blocks were all Windsor blocks...thanks for the info!!