Yeah, you need to slow down.
I wouldn't put the bridge on or even think about strings or a setup until the finish is perfect. Doing a full setup and then having to disassemble the guitar to wet-sand the finish strikes me as a bass-ackwards way to do things. Patience!
And "the drill press operator" screwed up? You had somebody else drill the holes for you?
When things are supposed to be evenly spaced, and even one of them is off by a fraction of a millimetre, it throws everything off. The human eye will pick stuff like that up. The ferrules may not be "too far off", but they look awful.
You've made some big improvements on this project... overall, your Tele looks much better than your previous efforts in terms of the quality of your joints and how it's put together. But then it falls apart in the details... the rough routing on the hollow chambers, the poor fit on the control cavity plates, the mis-spaced ferrules.
Patience!