If you run the base coat then you have a real problem somewhere. Either in the gun or how you shot it. Base does not go on thick. If you do you have to sand it and reshoot base over the panel, like entire door.
Clear is where you might get runs. It goes on wet. PPG is great stuff. Use the Omni base and then spring for the top of the line clear. It is awesome and you can buff it out to look like glass!