I just went through this, first time I ever rebuilt a jet ski engine (done motorcycles, not much different).
I was apprehensive, but splitting the cases is dead simple. Remove bolts, but leave the long bolts around the starter area and other side in, but about 1/2" unscrewed. Tap them with a rubber mallet and the cases will come right apart. Pull crank out and set aside. Check for burnt bearings or obviously damaged and loose bearings. Be careful not to damage lab o-rings on center bushings. Spray cases down with brake cleaner and wash with soap and water, remove all of the previous gasket material carefully with a razor blade.
If you ended up spraying the crank down with cleaner to check bearings, etc, be sure to re-oil it so it doesn't rust. If you are not going to inspect it, but just hope it's good, just wipe it off and set it aside but don't degrease it.
You can leave stator wires in place, just try not to get stator too wet. If you want to remove the stator wires, you can use a small screwdriver to release the pins from the plug, and spray the wires under the cover with armor all and slide them out through the rubber seals. Not worth the hassle, but I had to do it because I was switching bottom ends.
Make note of where the washers are and the directions the seals were installed, this is important. Make sure mating surfaces are perfectly clean and dry. Feel with your finger for any rough spots, dirt, old gasket material, dings, etc.
Re-assemble, install new seals (in correct directions) after greasing up shaft and seal where they meet, make sure cases go together cleanly. Spread a very thin film with your finger of Yamabond or Hondabond 4 (or 1211) on one case half. Cover the entire surface but very thin, you do not want it squeezing out everywhere.
Do not use the bolts to pull them together if they are not mating. Test to make sure crank spins freely, there will be some resistance from the new seals. Remember how it feels, it should not change as you tighten the bolts... tighten them lightly but not tight, continue to rotate crank and check for binding.
Now torque bolts to specs in manual (I think it's 16ft pounds), in the pattern shown (X patterns moving out from center).
Of course to do it entirely right you would need to spend time inspecting the crank, but tought to describe in one reply. Checking the bearings and connecting rod side and end play is enough to get you in the ball park. You can hold one connecting rod in a closed fist lifting the crank slightly off the table, smack the top of the rod firmly with the palm of the other hand and listen for a "clink" where it meets the crank. If you hear it, the bearing is probably worn. You will first be fooled by the clink sound of the bushing at the center of the crank with the o-rings on it, or the sound of the other connecting rod moving. Have someone hold them so you can hear whats actually going on. You could probably youtube that procedure.
When you are done re-assembling, install the top end and intake and exhaust headers, block with rubber plugs. Install spark plugs and connect a small pump with gauge (a popoff tester works), to the pulse port on the side of the case. Pump up to 8 to 12 PSI (no more!) and make sure it holds pressure for 2 to 3 minutes.. (it will slowly fall a psi over 5 minutes or so). It will take a lot of pumping with the pop-off tester but hey it's one less tool I need to buy.