I would helicoil every single hole you can get to when the cylinder is off. My buddy had a XR500R a few years back and when he had the motor out to the Honda shop they told him he had a couple bad holes and they recommended on a bike that old doing em all so that it would not be a problem in the future. It saved him a lot of heartache.
I had an '84 XR500, the same thing happened. I took it apart, said piss on it and had EVERYTHING helicoiled.