my suggestion is based upon your available investment
To me, older bikes are a cross roads. You can invest more in them than you will ever possibility get out of them, so i would decide my investment goal, then run that up against my hold on to the bike goal to see how to respond.
If investment is desired to be low, do a decent rebuild on what you have or a 98 kit, have a shop do a decent clean up on the heads and put it back together. the 2000 bottom end is pretty good.
if investment is desired to be more than above, pull it, split the cases, put a crank in it, go 107, have the heads done and decide how you want fuel delivered. Delphi or Carb. Make those changes and be done.
if you think you will not hold on to the bike. I would not put a ton of money in it. If it is your dream bike and you will never sell, then its a different story.