Oh boy...problem is that what you see is the tip of the ice-berg. Assuming that you don't want to sand off any paint at all, you could try to nuetralize the rust with something like Ospho, then nuetralize the ospho with baking soda and water, then dab on the clear coat. If you have any bubbling, I think you're stuck...either leave it alone or start peeling back the bubble and be prepared to do some spot priming. As for the hole proper, sounds like you plan to leave it? You could fill it with something like POR Epoxy puddy or even JB Weld, but both would require you to nuetralize the rust first and would look best if you put on some touch-up paint (which won't match what's on there now, but it might be better than nothing).
