OK, so I have had damage just like this on a 750 motor. The biggest concern in that area is whether the crankcase has been pushed in enough to come into contact with the transmission gears, the clearance at that point is not very big and it only takes 1/2 inch or so before the case is in contact with the gears. At this point your gears will begin to machine a nice arc into the inside of the case. After a while of driving like that your oil will be a nice bright silver from all the aluminum shavings
Ask me how I know this
So, I can confirm that sealing this crack with JB Weld
WILL in fact work. I cut a piece of sheet steel into a patch and JB welded it in place. It held up through a full riding season and then some, couple of thousand miles I figure. Once I changed my oil and saw the aluminum particles I decided it was time to give it up and just rebuild the engine, and that's where I am now. When I pulled the engine apart I had to chisel out the JB weld, it was still sealing the area just fine.
Now, having said all that, I'd recommend trying to source a replacement motor if that's within your budget, it probably would be cheaper than trying to repair the existing one, and safer than the JB Weld routine.
cheers
mystic_1