I was worried about possibly bending the throttle shaft when peening
Yes me too. If you're wacking it hard enough to peen, it's also hard enough to make scrap metal if all is not right! :-/
This morning I inspected the closing of the butterfly with the morning sun and all is good. I put it on the bike and now I can adjust both carbs with the idle mixture screws.
I believe the rough idling was the throttle butterfly all along and should have been repaired in 1/2 an hour and not the many days I took. I learned bunches of stuff about the carbs and never once did I scream in frustration " where are the Mikuni's".
I'll adjust all the cables now and get her on the road. Thanks to all for your help as I blindly struggled to completion

Now I can go back and worry about the original issue of it idling at the 3000rpm mark, but not today.