Crankseal replacement

Stop right there.

Go buy a puller from a bike shop. They should cost ~$10 for an accessory one & will fit 90% of Japanese ignitions. Run a bit of grease on the piece that pushes the crank-end to help protect it & some oil on the threads to protect them.

Do as David says. The reason the flywheel is so hard to get off is the woodruf key holding it in place. The puller is the cheapest and easiest way to go.
Also I hope you did not stick anything long into the holes on the flywheel to hold it when you got the nut off. You can damage your magneto coils that way.

Holy cow! This makes me shiver!

Whacking a flywheel with anything? They only cost $500+..and whacking it can ruin (destroy, lessen, make useless) the magnets that make your bike go.

Air tools make the job much easier (WITH a puller). Note the left hand threads! (Don't know about your particular bike, but I think they are mostly LHTs).

BTW..when you put it back together, ensure the key indeed stays IN the slot by sticking something in the key-way (small screwdriver, piece off wire, etc). You'll easily feel it if it's there.

You CAN get the flywheel on AND back out the key in the process. You don't wanna do that!

Tighten the flywheel per spec or you will likely shear the key. That will happen at the apex of your ride (greatest distance from your rig).

RE: anything else when the cases are apart.

Well, a lot of things, actually. Read Eric Gorr's write ups on site regarding the subject. (click on his ad to the left..then go to forward motion).

A thread in the archives of this site mentions a critical and often overlooked issue regarding seals. Make sure they are installed in such a way that allows the bearings to be oiled (clear the holes in the cases).