Refinishing an acoustic....Primer?

[sjaguar13]

I need to refinish my Epiphone acoustic. The neck broke, so I glued it back together. The problem is you can feel the crack. If I fill it, it's going to be obvious it was broken. It's obvious now. I was thinking about filing it, then painting it because the guitar has already been sanded. It's no longer shiney. Would I just paint it the way it is now, or would I prime it? I don't want too thick of paint. Would it be better just to shoot a coat of clear, sand it until it's a littly scuffy, then refinish it? The guitar itself was natural wood color. When the clear was sanded off it, there is little scratches, but they can only be seen while holding it at the right angle under light. Should I try to sand that completely smooth before clear coating, or is it better that way so the clear sticks? I just don't want the clear to magnify the scratches.