Don't tighten that upper shock nut with an impact gun, even if you could. You can easily destroy the nut or shock doing this. Impacts are great for taking an old shock off you're going to throw away but, not for installs. Use hand tools. It doesn't need that much.
You've gone through lots here but, it sure sounds like a bad shock install or worn shock. any wetness on the shock itself?
You sure it ain't the exhaust pipe hitting the frame or PHB brace? It's possible here when you install axlebacks.
No wetness as far as I can tell and the rebound rates on both the konis and stock ones seem to be okay as well.
I thought it might be the axleback but I don't see anywhere it could be clunking and there was no clunking initially with the stock shocks and ultralites.