Hi DrJack. Welcome & happy holidays.

Sonic posted before I finished typing and there's a bit of overlap in our responses, but I've already typed it so I'll post it anyway

I'm not a bass player, nor have I built one but all you your questions are relevant to any build.
I'll try and go through them in order:

re: finish -
I have no experience with the Rubio Monocoat and didn't even know it was available in Australia until now.
It's quite expensive here, but sounds interesting. As for oil based stain and Tung Oil (essentially polyurethane) is common, tried & true combination. FWIW, what is sold as Tung Oil nowadays is not truly Tung Oil, but that's another discussion.

re: knobs -
Does the offending knob happen to be the one with one of its 4 mould partitions filled in? (hope that makes sense)
If yes, my guess it that the hole for the pot shaft is not allowing enough expansion to accommodate the shaft properly.

It may just need a tiny bit of sanding. Just wrap a single layer of sandpaper around the blank end of a 5.5mm drill bit and twist it by hand in the knob hole. Try to fit and sand more if needed. I don't think it will take much.

re: input jack -
The OD of that long panel jack should be 12-13mm and the jack hole in teh body may just need a bit of a clean up.
If you have 1/2" drill bit (a twist drill bit, NOT a spade bit), just try running that in & out and see if that does the trick.
If you don't have a bit that large, You can do it with sandpaper or a round file, but just be careful to do it evenly so you don't finish up with an oval-shaped hole. Again, I don't think it will take very much removal of material.

re: pickups orientation/height -
I concur with Sonic about the orientation. If I were doing the build, I would route a channel for the leads to run through so not to interfere with any downward adjustment, but that may not even be an issue when final height is set. The difference in height between the neck & bridge pickup may also be ok due to the angle of the bridge and strings. A Les Paul bridge pickup sits up higher than the neck just for this reason.

Hope this helps, and look forward to seeing your progress.