98' and up all have their speedometers run from the rear diff NOT from the T-Case like previous years. So if you where to get a 98-01 you would have to figure out a way to get a speed sensor to work. Since your 9" wont have one on the diff.
The transmissions in the V8's are 4R70W's. Its more or less the same tranny that's in all the half tons. Very strong and most on here never have to touch them until 200K+. Also has a nice low 1st gear for great wheelin. (If you do the 4406 Swap for low range) Any questions on them look through the Diff/Transmission/T-Case section. Also the 5.0L V8 drive train has been voted on here as by far being the strongest/longest/ and most reliable drive train put under the Explorer.
As for differences, a few you might care about or might not. The 98 and up years have a different lift gate and tail lights than the 97 and down years. The 97 and down years are the ones with the twist T handle to open glass and the lift gate. 98 and up is a lever under a trim piece. 2nd the 99 and up years have the better cast iron exhaust manifolds on them. The 98 and under had tube style ones that crack and leak. (I replaced my 98's with the cast iron ones, also a hair better flow and MPG) And third the 98 and up years have more of a medal torsion key pad that doesn't wear out like the 97 and down ones. When they are bad the just kind of clunk when turning into driveways and things. Other than that they stayed pretty much the same, minus a few same things here and there.