If I remove the flywheel (to check something on the magneto that I can't see without removing the flywheel), will I have to recheck TDC and reset timing again? Or can I just reinstall the flywheel?

Points? Just re-install.
Assure torque is is up there, bang it a few times.

cliff

Thanks, Cliff.

Keep the bangs to a small hammer i.e. screwdriver handle.

Multiple times while torquing.

Let it/them find centers. This is the real locking feature, taper.

c

Cliff, you are talking about banging the points' lock-down screw?

So long as the locating key is in the crank you'll be good to just sit it back on there. If you've not altered the points then nothing should have changed--in a perfect world. Providing the points have gap within spec & assuming it was running ok before. I tighten them holding the flywheel solid with a holding tool. I'll find a pic later. They like to eat the crank key for breakfast if not super tight.

Yamaha recommends checking timing every time you remove/replace the flywheel.  I usually don't but there is a tiny bit of slop in the key and timing can change a tiny bit.

Personally I never hammer or tap on a flywheel or crank end.  Crank is remarkably easy to knock out of true and magnets can be weakened by hammer shock.  Tapers need to be clean and dry.  I run the engine a few minutes and re-torque.  Then after about 30 more minutes of running, I check torque again.  (This is the old Husqvarna flywheel installation process which if you didn't follow would often result in a sheared flywheel key.)  Probably overkill but I've never had a flywheel come loose and shear the key.

Here's link to an old pic of my 360 tightening with a good solid feel of the socket handle. Did you have the correct puller? to remove it.

photos.app.goo.gl/Cc5neaoxi1pwvg478

RT325, yep, I have the right puller. Thanks, all, for the suggestions.