If you sand too soon you may push any dust deeper into the lacquer and also run the risk of gouging the preparation coat. With the imperfection corrected reshoot that area. When you have the white primer completely covered with color shoot a couple more passes to doubly insure the coverage is complete. Before preceding with the clear coat it may be necessary to flat sand the color coat. If the color coat appears smooth sanding before applying the clear coats may not be necessary.
Definitions are in order here.
Overspray refers to paint on the surface that dried before it reached the surface. Orange peel is caused by the paint drying before it flowed completely smooth and flat. Orange peel will take more aggressive sanding. Sand until the surface is smooth and all the bumps are gone. When the sanding is finished wipe the guitar with damp towel to remove any dust.