One of my favorite tools for removing runs are little metal blocks called Run Blockers. They are made by Motor Guard and they have saved my butt numerous times over the years. Basically, they allow you to focus your sanding on the run itself. But you have to be careful as you can end up sanding too much in that area and go thru the clear.
Sanding runs in clear is not beginner stuff. Its not easy so don't get frustrated when you sand through, cos you will. When I have to sand a run in clear, 60% of the time, I go through. This is why I always opt for having to buff some slight orange peel rather than get it too flat and having to sand a run. Getting clear to flow perfectly every time is unreal hard. Gravity is not your friend.