Thanks for the advice.
I was surprised that neck and body didn't match better. Like I said the neck is a Johnson, but the end looks the same shape as the one on my Fender. The body isn't actually the one shown by the seller (MusicValue) on eBay but the neck pockets look the same. (This one came with a bridge and jack already installed - nice! So, I'm certainly not going to complain.)
Just the corners of the pockets are rounded but the end of the neck has a nice, gentle radius all the way across. As long as it doen't matter, I'll just fit it tight in the middle and shim the sides (very slightly to get a real tight fit that way. I'm also going to have to fill existing screw holes and re-drill to get a good match. I plan on glueing wooden pins in to the old holes.
Strangely enough, the screw holes on the Squire pickguard that I'm planning to use don't line up either, and the bottom tone pot is a little too wide for the routed cavity. Guess that these are adjustments that I should expect to make?
Given the intonation adjustment that's available on the bridge, I measured to the saddle, but assumed that exact didn't matter. Right? We can take care of minor differences with that adjustment?
Follow up question on the intonation... I understand in principle what we're trying to do when we adjust the intonation on each string; I understand how to tune the open string of course; now, how do I check the 18th(?) fret for correct tuning? I'm using a Crate CT-1 tuner that auto-detects the string and shows both low/correct/high lights and a needle-guage. I need simple, how-to advice here, not a theoretical discussion, please. (I'm a beginner guitarist, as well as a beginner builder.)
Another follow up question! I'm actually using a lefty neck (with a gold righty body, like Dick Dales). I realize the low strings are going to be longer above the nut, but can't see any reason why that matters. Are there other potential problems with this combination that I should be aware of before I start drilling holes and driving in screws?
Don't ask why! It's my first project, so it's supposed to be a learning experience, right?
Thanks, again.
--- Mark.