Brian,
unless I missed it, you didnt specify what kind of paint you are spraying.
if it is basecoat auto paint, you will most likely want to spray another light coat of base. sanding base and then clearing it can lead to some unsightly scratchs as the base doesnt sand cleanly. 1000 grit would likely clog rapidly and would most likely cause "scuffing" streaks in the base that will show when you clear it. You would most likely need to sand it lightly with 500 or 600 paper and even then I would want to respray it.
If its dope,, sanding with 600 wet then clearing would likely work fine.IMHO The clear dope you put over it will to some extent reflow the color as you lay it on and the scratches will disappear. or so has been my experience.
In simple terms, like Randy said, sand it with the expectation you can clear and be done, but keep in mind you may have to respray,,