honestly not much is different... just (now dont quote me and let someone else verify this) make sure you back off the rebound setting to full soft so the needle is backed out all the way so you cant bind anything. also back the preload out all the way as well (full soft) to make life easier.
Other than that its all the same... you will need to cut the spacer (might of already been cut for you) to the right length as the 02-03 and 04+ have the obvious difference of preload adjustment and as such their preload spacers are different. Id be willing to bet that the preload spacer on the 02-03 is the exact amount of half of the preload adjustment on the 04 more than the 04 spacer... so that preload is set in the middle.
There is no relationship between early and later spacer lengths, as the spring lengths are different and that the later fork caps have a longer effective internal projection distance.
Simply follow the instructions to figure out the needed spacer length, although I would not use more than 15 mm of internal preload. Yes, have the ride height adjusters fully backed out when you are doing your spacer length determination, do not do it mid setting.
As for the rebound adjuster, the way to do those before you disassemble is as follows :
Back off something easy to remember and write it down, either a half or full turn.
Then open up the top and loosen the rod locknut from the fork cap.
When you reassemble, turn the rebound adjuster back in by the same amount.
Then very lightly run the cap down on the rod until it barely loads up on the rebound needle.
Again back off the rebound adjuster by the half or full turn.
Then bring up the rod lock nut to seat against the cap, and tighten it.
Fit the fork caps and lightly tighten.
Gently close down the rebound adjusters until they barely seat, then back out 2 turns which is your starting point and you'll always have to go "firmer".
Try 1/8th increments from that point on.
You should not have to go firmer than 1-3/8ths (out from fully closed).
The factory manual is not of much help for any of the work you will be doing, aside from changing seals and bushings that is.