just got my 98 back from JBA with a new T-56 in it two days ago, i love it. you need a shorter driveshaft and different crossmember as well. you also need a new bellhousing as they differ between the T-45 and T-56, but most places sell them together. D&D is the place to get it, i got mine from a buddy that works with ford so i got a deal on it. install was pretty cheap. i have 4.10's and haven't had a real chance to open it up yet but if you get gears i would probably go with 4.30's. also, you might want to do a clutch while your in there, saves money.
P.S.---you will need a Dallas MustangSpeedcal to get the speedo dead on, even with the speedo gear switched over mine was off by 20mph by 80 mph.