Hi Russ.

Wonky tuners. Unfortunately every 6 in line headstock has the wonky tuner holes. It makes zero difference to the playability and sounding of the guitar. That being said you can plug the offending holes with doweling and re-drill. Most likely you'll need to either paint or veneer the headstock if the tuners don't hide the doweling. You might as well give veneering the headstock a go, its well worth it. You can buy a marquerty pack for about $20 - $30 and get a heap of different veneers for headstocks.

I'm not liking the look of that copper wire sticking out of the humby. Test the resistance (or continuity) with a multi-meter, If she don't work, chuck it. same with the single coil. If you need a new PBG single coil or Humby, let me know I've got a stack from various kits I can send you some. Other wise there might be a forum member in Vic that has some spare.

when checking the bridge and neck alignment prior to finishing, I get some plastic tubing from the green shed and wrap it around the bridge posts to hold it in place. I don't like putting in the bushings before I finish a guitar.

Its pretty typical to have some play in the neck hole. you'll need it to get the neck square and the alignment correct before drilling. Its a bolt on neck so it matters none and the pickguard will hide any gaps. if you dont like it I would shim it with some veneer offcuts from said marquetry pack.

good luck mate