The fly side bearing race is toast. The new bearing will come with a new race, so be sure to use it.
If you don't already have a bearing splitter, it's worth the $60 to get a cheap set at Harbor Freight/Northern Tool/etc. Removing that race without it is absolute misery.
The Malossi Sport Mk II is definitely the correct choice of cylinder this time around. If you wanted to go crazy, reed, etc., then you'd want a Quattrini M244, but that's a whole 'nother conversation
You're going to want to get some sharp grinder bits for your Dremel to do the port matching, but that's only scary when you're new to it. Ideally, you'll expand your intake timings a bit while you're at it. At the very least, clean up the intake and widen it a little bit.
Of course, either of those mean you're going to need to either do a full teardown of the cases and/or tape the crap out of everything to keep swarf contained. Given that it'll be aluminum vs. steel if swarf gets in anywhere, a little bit isn't going to hurt you, but less is still better in this case.
And for potentially-missing parts...
- Check the gear stack clearance and order a new shim if it's not within tolerances
- a new cruciform if you haven't already ordered it
- Take a look at the motor mounts. If they're ovaled or just really hard, replace those. Makes a huge difference in both general comfort and handling
- Replace the kickstart o-ring so your bike won't try to mark its territory with a drop of oil every time you park it.