will 01 GT 5 speed work on my 98 4.6?? i need to know ASAP!

One note, this may a bit complex in your case, the 99-01 T45 used an electronic speed sensor, the '98 and before used a mechanical one, this may be an issue hooking up your speedometer, etc. Given that this is going into a '99 car, I am not sure exactly how though.

Ike

p.s. the change from the T-45 happend mid year 01
 
it could be a t45 out of an 01 if it was an early production , look on the passenger side of the tranny , if its a T45 , it will say Borg Warner under the gear shifter , if its a tremec 3650 it will say tremec on the side of it little farther forward on the same side of the tranny , I am not sure about the bell housings , I havent seen any major differences on a T45 and Tremec set up , both of the them say tremec on the back of them , so they might be the same , so might not make a difference either way , have to check into that.