If I was working on that guitar, I would go ahead and touch up the entire top. It looked good bare, but as soon as you painted it, all the flaws on the carve showed up big time. Get a grinder and some flap wheels and practice on some scrap pieces. Once I got use to them, they are the best tool I have found to shaping. Once you get it close to perfect, sand it all the way to 400 and prime it. Get a good primer also if yo u are using automotive paints. Don't go with cheap rattle can stuff and have the paint lift it or end up with a chemical reaction that will make the primer turn to rubber.
Like Wes said, also don't use that "glazing putty" it is the worst thing you can use. It is intended for filling up pin holes, and not contouring. Get a 2 part glaze, Dolphin glaze is cheap, and flows nicely for guitars. Bondo is good too, but you have to know how to spread it as it is less forgiving as glaze, with glaze having the added bonus that it sands as easy as primer does.
Use guide coats once you prime it to check on low/high/un even areas. Once all is good, then paint the guitar. All you should need is may be 1 dust coat and 1 full coat of color and 1 tack coat and may be 2-3 medium coats of 2K poly.