For the scratches, you just need to step up to a finer sandpaper. Personally I wouldn't have gone lower than 100 grit either. You could can get by wetsanding with 400 grit and then 800 grit, but if you want it super smooth, take it up to 2000 grit. Going to 2000 is overkill though unless you trying to get it smooth as glass. I'd stop at 800 though if you're just using spray cans and not planning to color sand and clearcoat. For the high areas, you just need more sanding until your satisfied. Take your time though, it's easy to get caught up and take too much off. You can always fix it if you do, but thats just more sanding to do.