Those don't look as bad as I expected from the original post---focus is placed a little forward or back of where you wanted it, but nothing I wouldn't expect from some struggles dealing with the shallow DOF of a large aperture in a large format.
It seems like that nice vertical pipe should have been an extremely easy target to focus on with the horizontal split prism, though. I wonder if you aren't shifting your posture a little bit back or forward after focusing---the kind of unsteadiness that you can get away with if there's more DOF, but in these examples it would be pretty easy to lean just a little and get this amount of shift. A heavier camera might exacerbate that; so might some little things that people tend to do while focussing, like holding their breath (don't do that).
I'm also led to compare to guitars, but I have the opposite experience from you. On the old dreadnought that I've been playing for the last 25 years, I'm a badass, or at least I can get myself into that playing space where I *feel* like a badass. When I got a really good, really responsive fingerpicking guitar, I seemingly became a much worse player, because all my bad habits were audible! Just so with focussing in larger formats---the little bit of slop that you wouldn't have noticed on a 35mm camera suddenly matters.
The largest format I've ever shot is 8x10, but I'm told that the Absurdly Large Format people---20x24 and so on---basically need to go over the ground glass, micron by micron, with a loupe, deciding *which* eyelash is going to be in critical focus. Phew.