Before welding on the Rockers it looked like a good idea to weld on the transition piece. That way I could paint the inside and ensure it would be coated well. Then it would just have a weld seam against the A pillar similar to the rest of the rocker panel. I did not weld on the end cap. This was likely welded to the rocker before assembly to the car at the factory. I will leave it open so I can paint, or at least attempt to paint, the weld seams on the inside of the rocker. I picture moisture pooling up there and don't want any bare metal.
After that we primed the parts of the car that would be inside the Rockers and fenders. For projects where they don't remove these I don't see a lot of talk of how they get the paint in there. Or when they made the car originally. Perhaps that is a reason why they rusted so quickly? Who knows. I know I want it all painted/sealed.The weld flanges were all taped off and the surfaces primed (still taped off in the pictures). This time we are using a white primer.