I'm pretty sure that replacing the head is beyond my capability as a mechanic. I'm also pretty sure that welding that flange up in place will destroy the head. I'm also pretty sure that those frame points are load bearing and essential. Any ideas before I declare this a loss? Or is the remaining amount of aluminum meat enough to hold it together?
First, I want to observe that aluminum meat is a product destined for failure.
You've got options.
Do what Chaos suggests and be inspired by the Dude; but don't use the bike as a scrambler. Enjoy riding it in free air. I'm guessing that many here will never feel the need to swap an engine or even remove a cylinder head. You might be one of those; the JB Weld may be good enough, this engine may be good enough and a crack in its repair will show eventually show. Decide then. It's currently not a "track day" bike.
Ride the bike to several welders and show them the problem. Listen closely, compare what they say then decide.
If it appears that this bike is likely to require a lot of bucks to be roadworthy, just say "Feck it", sell it for whatever you can get and mark it off as a lesson learned; however,
you be the one to show prospective buyers this defect. I made a couple of bad vehicle purchases early on when I knew nothing about engines, drivelines, brakes and body rot. You eventually learn about what you need to inspect and what you need to ask when buying used; otherwise, you buy from somebody with an enforceable warranty, or you buy new stock.
Someone will buy it and, if the rest of the bike is decent enough, maybe will install a reconditioned head on it then ride it to Tierra del Fuego; maybe even go there regardless of repair if they're desperate enough.