There are patch panels available for that inner cowl panel. You're on the right track there. Cut out the rust and weld in new metal. For the A pillar (below the hinge pocket) scrounge up a small piece of 16 gauge steel and cut a piece to match what you cut out to get to solid metal. Butt weld that in.
As far as the rugged weld between the A-Pillar and rocker panel, that looks pretty typical for the factory welds. I had my cab sandblasted, and there were still pockets of weld flux in those weld joints. Not quite birds**t, but close on the weld quality. If it's solid, a little filler will make it look pretty. Or like bartamos said, dress it up with a grinder.
