Bag (ziplock) and tag (write on the bag) every group of bolts you remove. Do this and you will thank me later.
You will have to replace the main bearing bolts. They are torque-to-yield on the 954.
May as well look at the clutch. Check the metal plates for bluing, indicating that they got hot. Make sure you put the clutch plates back in same direction they came out. There will be a sharp(er) edge on one side than the other.
You have to remove the clutch basket to get to a bearing retainer that spans the parting line between the upper and lower cases. Can't split the cases unless you do this.
Speaking of splitting the cases, don't forget about the bolts that on the top side! They are towards the back half of the engine and go through to the transmission area. In thought I was gonna bust the cases trying to get them apart. I turned the engine over and dammit, there they were.
I took the clutch plates out and stuffed rags where the clutch plates were. I packed them tight with a screwdriver. Then I used and electric impact wrench to remove the center nut that hold the clutch basket on. Don't mess with trying to use a breaker bar on that.
I would check out the shift forks for signs of obvious wear.
Check the shift drum too. I had a bad one in the Craigslist motor I bought this summer.
Check your oil pump pickup screen for debris. I had a bunch of it from the bad gears (2nd gear on mine). I ended up replacing it.
Use Hondabond HT on the parting line between the cases when you go back together with it. Do not use Hondabond 4 for that or any other gasketless application. Only use Honadabond 4 for applications that have a gasket.
If you are thinking about replacing the CCT, whether it be with the stock one or a manual one, now is the time. It's a bitch to get too after the motor has been reinstalled. I had to drop the exhaust and lower the engine do that.
That's all I can think of at the moment.