When I realized what had happened, and basically thumping my skull for being stupid, I was almost ready to give up. What I should have done was do the finish welding in place on those upper welds which wouldn't have burned anything... The foot pads would have been finish welded on the table, they wouldn't make anything move anyhow.
So, it seemed like I had few choices. I could cut off all the tubing and start all over again, that would suck. I could trash the whole stern rail... that would suck even more. Or I could suck it up and figure out to fix it... besides, my YouTube user name is 'SteelDoesMyWill'... time to own it!
So I was able to get the factory bolts back into the original feet on the transom, and then line up the and pin the bolts on the outboard sides. The two new feet were still floating, but the port side was close enough that I could put the 1/2" eyebolt in and get the nut to thread. Cranking in down with a socket wretch helped pull the whole thing into alignment a bit closer, especially flattening out the top rail. At that point it was looking better but the starboard foot was still floating and about 1/2" off from the mounting holes. There was no way I could muscle it into position to get the eyebolt lined up. So I ran to Home Depot and got some new heavy duty DeWalt clamps that can be reversed into spreaders. These helped a bit but I knew it was the welds on the horizontal that was keeping everything tight. To relax the tubing and allow the spreader clamps to force the warped vertical tubes back straight I had to do relief cuts on the underside of the welds. I used a fine cutting wheel on my Dremel to follow the weld lines around the bottom half on each side. After that I evenly applied pressure to the two clamps and forced everything back to a point of alignment where I could get the second eyebolt in and crank it down.
Here is the result with everything pulled back into shape, both of the spreader clamps still in place;
A close up of the relief cut on the bottom half of the horizontal tube weld;