Sounds like a really good first effort! You also ran into a bunch of common problems, and it is impressive that you solved some of them without power tools! The problem you ran into with the pickguard and control plate is a common one. Holes almost never line up with aftermarket. Also there are some small differences between Asian-spec parts and US-spec parts. I had that with a Jazz bass pickguard, where I had to modify pickguard to fit the control plate. Same with the pot holes. Although the CTS pots are made in Asia, the shaft is US spec, but your control plate is Asian-spec...so slightly larger where it meets the pickguard, and slightly smaller holes. What did you make the pickguard out of? It's very unique looking and kind of cool. I thought it was perloid at first... No one will ever see the cavity, but it looks pretty good to me!

Sounds like the Pentax prepared you well. It helps that you are using quality parts and going slow. I have found that I can do most things if I go slow enough...although going slow can also be a challenge!

One of the great things about starting with a kit or cheap guitar is that if you don't like something you can generally fix it. I am with your son on that. A well set up cheap neck can feel better than an off the rack expensive neck. Now he'll have a one of a kind guitar, with a classic Tele bridge, but some interesting switching and beefier neck pickup.