Does any body know if engine cases are matched and line bored?
Or can you take a upper case from one engine and mate it to a lower from another?

I do not see any alignment pins in case halves.
So is the only alignment of halves from the bearings?

not completely sure with all brands but skidoos are def case matched and you usually cant mix and match them, they have alignment pins on them....and so do the polaris cases we have.....