It's really not as difficult as people think. It's a matter of a straight line and some general measurements.
You really only need to worry about getting the neck alignment right, which isn't even hard if you wait to drill the bridge holes until after the neck is glued in, like they used to do with Les Pauls (even if they did pre-drill the stop-tail holes). For newer production, like Mayfly's Junior project, CNC means that you can safely drill all the holes since the only way you'll mess it up is to butcher the neck tenon. Which I am sure some people do.
For Fender-style neck joints, as long as you have a good center line to work from (and use it) your neck pocket and neck heel should have no problems (that factory necks don't have). I suggest using some tape on the flush-cut bearing, so that your pieces are plump and you can work them down incrementally until you get the fit you want.
I prefer everything to be perfectly square, but don't always have that option. But by working from a specific plane, it gets easier. For example, cutting the neck out using the fretboard plane (but before gluing the FB on) means your sides will be square (enough) to the face. Most wood is planed square enough, and I never worry about, for example, Warmoth neck blanks like I used on the '6C.'
Even if/when things aren't perfect, you still have a surprising degree of adjustment available with the bridge and/or neck pocket. It's nice if your fretboard is perfectly level with the body top. But does it really matter? No. That's why bridges have height adjustment on each side.
I even have trouble cutting the headstock angle square to the neck plane. But looking at things like the Torzal design, I'm tempted to build a 'wrong' neck just to see if it makes a difference.
Don't get me wrong; with the right tools I would always do it the 'correct' way. But I don't have the tools I want. So I need to adapt.
If someone wants to try a scratch build, I'd strongly encourage using as many thoroughly tested templates and jigs as possible. If you notice, I have ones for truss rods, the body shape, pickups, cavities, the neck shape and the headstocks. Routers make the work better. A drill press is pretty necessary too, though on a bridge like the Schaller 456 you can get away without one.
Shaping necks is not too bad, again given the right tools. The key is to go slow and spend at least one set of strings on 'tuning' the shape. Assemble the guitar and play it, and take away everything your fret hand dislikes. Is it right? Who cares? Is it right for you??? My necks are ridiculously huge, because it's more comfortable to me. No one would want to buy one, but I didn't make them to sell, I made them to play.
I really need to work on my tuner placement; the HGSEC build is okay, but I got the placement (or angle) wrong and it shows. I even used the placement jig I got from StewMacc, so I know the error is mine But next time I will use triangulation from both E string slots in the nut to each E tuner. I will also triple check the angle of the tuner side of strat-type headstocks, since I always think I have it then drill my way into 'wrong.'
On the Junior, I...
Oh wait, I haven't put that entry up yet.
