Spraying one coat then sanding it is asking for trouble anyway. You don't ever want to sand thru the clear, solvents from the next coat can get under it and lift. So be careful not to sand that clear too thin.
On those runs, you have to be careful to sand ONLY the run. Using a run shaver as mentioned is one way. If you sand the run, use a very narrow block and concentrate so you are cutting ONLY the top of the run and not the surrounding areas. Do it very carefully, just take your time and do it very carefully cutting JUST the run until it is level.
I would be wet sanding that run and not try to use anything else, you have much more control with a little block and wet sanding. Use a rubber squeegee (3M 05517) to clean off the water so you can see. Use it often, keep your bucket and sand paper clean enough to drink out of. You don't want anything to get in there that can scratch the clear.
Just be very careful to not cut the clear thru. If you do you have to be careful not to apply the next coat over that area too wet.