97-02 are 32RH, 3-speed autos (no overdrive).
03-06 are 42RLE, 4-speed autos (overdrive).
many regard the 32RH as more durable and having better drive-ability than the 42RLE.
I have a 42RLE. I can tell you that it's undergeared from the factory, and the gear shifting behavior is funky, especially the overly steep overdrive. As a result, you need to throw very deep gears at it to improve drive-ability. 4.88s for 33s, 5.38s for 35s...even 4.11s or 4.56s for 31s/32s. For a comparison, a 05-06 6-speed manual w/ 3.73s & 35s is overall geared the same as a bone stock 42RLE w/ 3.73s & 30s...if you don't use 1st or 4th.
The 32RH kinda has the opposite problem. You need to stay numerically lower on the gear ratios to keep the RPMs a bit lower on the highway, since you don't have overdrive. So 4.11s for 33s, 4.56s for 35s, etc. With a 30-31" tire, 3.73s would work fine. Some came with 3.07s tho, I think?
Either way you go, figure on adding an external transmission cooler. Also try to find a D44 rear, over the D35c rear.