There are different length tail shafts, I do not recall off the top of my head which cars have it, but that platform (Gran Marq, TC, CV) have a chance for a longer tail shaft. I think a v8 mustang trans will work up to 99. V6 trans is a different bell housing setup. I have a 2001 mustang trans in my car, but in 2000, I think they changed the number of teeth on the output shaft for the speedo. No bueno.
You can swap the tail shafts, but it is A LOT of work, if you aren't comfortable completely disassembling both transmissions to swap the tail shaft.
Take a tape measure to the junk yard and get looking at the overall length, or just the tail length. If you search the net, you should be able to find more info of what should swap.