If you're "filling" the crank in the area just under the carb, it won't even get hot there...The alcohol in the fuel will keep things nice and cool. The only time the area will get warm is after you shut down the engine and you get some heat soak...
The engines I previously mentioned were done almost 20 years ago, and are holding up fine w/ the JB Weld...
The balance shouldn't be effected unless you get carried away and use a lot of material (shouldn't have to ). What little you should need to use is so close to the rotational axis of the crank that it won't upset the balance in a noticable way.
I think most engines are a little out of balance anyway...I know some of their owners are!