Alright since fixing a few nagging issues and braving the possible fuel tank clogs I feel like this is really solid now, I blew the return out on both tanks so I know there is no obstruction and the left side is ironically running better than the right tank ever did.
Ethel pulled a full bed of tools to Vegas and back with zero issues, lots of city miles showing off to everyone. I put 450 miles that weekend on the truck and it never missed a beat. Since then I've just been piling the miles on. I had to change a water pump again but as before taking my time has paid off. I've tried to check the slack in the chain but I cannot see the chain from above so that'll wait.
Tugged our good buddy Dillon out of the bottom of a sand pit Sunday, absolutely surprised me with the kind of authority she did it. And then again the next 20 miles just trudged it home. Was able to maintain 45 on the roads which is about max in 2nd so a turbo is on the list now but I trust that this thing is good. I think I've figured out the surging and miss at idle is more related to either an air leak inline somewhere or just the pump being a bit worn, it doesn't effect anything else so I am not gonna worry about it. Happy camper right now. Ready to put her on full daily duty!