Matt, missed this. Using my phone to reply is tough, and lately I'm a bit hobbled with a sprained ankle to get downstairs to the computer.

Having done the first-ever Scarebird swap on the same car, ironically, that got the VI head, I know it well. Would laugh to find out whether they are still using photos of my hands and that car in their instructions. LOL. Anyway, the bolts you refer to are standard spindle bolts. They were intended, when new, to butt up against the grease shield and with an impact draw up tight with no need for a wrench or socket to hold the head. Getting them apart 50 years later, not so easy. They are Grade 8 and your replacement bolts should be as well. I don't know of any reason you can't get standard 3/8-24 grade 8 bolts and the correct style lock nuts. Tacoma Screw should have them. I've bought these from them before.

Kind of lost you regarding the lug nut paint issue. Maybe you'll figure it out. Pictures help.

I sort of like the 65 Falcon brake light, but it's a pain to add. The easiest switch to use is a 70's F100 switch and mount it by removing the rebound bumper stop up under the dash.

What is the rear leaf issue exactly? I've worked on a couple, but not aware the issue here.

Sounds like a pretty impressive list of to-dos. Will be fun to watch as you proceed.