If I were in your shoes, I probably wouldn't bother tearing this thing apart and doing any repairs. I would sit on eBay and wait for a reasonable motor to pop up. I already did this a few years ago and my eBay motor has been running perfectly since then.
Here's my reasoning: Whatever blew the hole in the case also threw debris all over the internals. If that debris clogged up any oil passages, you may have burned up bearings. If that debris got into the bearings before clogging up oil passages, you may have burned up bearings. If that debris got up to the cylinder walls then you may have to overbore. Boring and pistons aren't a big deal, but bearings sure can be. Especially crankshaft bearings, because they're nearly impossible to find for the CB650 motors. If the camshaft bearing surfaces are messed up, game over until you replace the cylinder head cover.
Add up all of the time and money on both parts & work sent out to shops and you may be paying for a new motor. It is a risk to go down that rabbit hole, and also a risk to buy a used motor. But I'd rather start with a complete cosmetically undamaged motor that spins to work with instead of one that needs critical repairs off the bat.
Others may disagree, but that's my take.