you have to replace 2nd and 6th gear, and all the circlips and the left sift fork forsure, id say replace the shift rod and washers too, youll need to get all the gaskets as well(oil pan, timing, stator, clutch), new orings for lower coolant pipes, new exhaust gaskets
i just finished this rebuild on my 99 last week, hardest part was getting the flywheel off had to take it to 2 different shops, as well as putting the engine back in the frame when your done...had a buddy bring a floor jack and help me, wouldnt have been able to do it otherwise.
the clutch and carbs can stay on but there will be a bracket under the clutch on the lower case that retains the pump chain that has to be removed after you split the cases and before they can be completely seperated. i was able to keep the pump sprocket on and just wiggle the chain off.
cost me about $400 parts and fluids
i had to replace: 2nd 6th, left shift fork, fork guide rod.... gaskets orings circlips ect...
went for a ride yesterday 2nd is strong but found a leak at the oil pan breather hole so have to remove exhaust, oil, and oil pan to fix leak so be sure to give yourself an extra $100 for any f#ck ups
check out supermotojohn on youtube he does full rebuild so just pick out the video parts you need if you want some idea of what to expect...