We have cleaned the walls and then primed. Had to sand and then mud. We then cleaned and primed with bubbles coming out again. At wits end here- what to do?

My garage doors are all cedar, stain has faded in some areas. There also looks like a clear coat finish had been applied over the stain. How do I get the stain looking even. Is there a way to do this without having to refinish the whole door. If not