I am pretty much in agreement with the others, but thought I might be able to contribute a little clarification...

Quote Originally Posted by nathan View Post
1. Measuring from the inside of the nut to the middle of the saddle seems to give me my 628mm scale length (image 1). Is this the correct way of doing it, and is that all I need to do? Measuring from the inside of the nut to the middle of the 12th fret was 313mm, not 314mm, which I assume is totally fine?
I think it's pretty safe to use 628 for the measurement from the bridge-side-of-the-nut to the nut-side-of-the-high-E-saddle, as long as you back it off a hair. Personally, I would have it closer than 75%, because its the low-E I worry about, not the high-E. The high E is the only one for which you have an exact measurement in advance. A true Gibson scale length would be a little closer to 628.65mm. That means if the high-e saddle is 628 with the saddle all the way toward the nut you might have to back it away from the nut by 1/2 mm or so to intonate. As TD indicated, the more important thing is to have enough adjustment toward the strap button on the low-E side. The challenge is the low E where you are never completely sure how much backward adjustment you need until you have it glued and strung.

Quote Originally Posted by nathan View Post
2. I'm a little confused about the neck heel. In profile, the bottom of it seems to have an angle & curve when compared to the very end butt, so depending on which one I place flush it greatly affects the angle of the neck (image 2 & 3). The cavity for the neck is dead flat, so I'm unsure how it should be sitting in the neck pocket. The cross section of the heel has some very slight curving towards the edges as well (image 4).
Most important thing is for the glue to get a good bond on the sides and bottom. If you put your clamp over the frets it should be fine. The thing to check is to make sure that there is enough downward adjustment on the bridge with the neck in place. It's OK if the strings touch the fingerboard with the bridge all the way down. You can always adjust the bridge up. But with the neck clamped if the strings are high with the bridge all the way down, that could be a problem.

I don't think it makes a difference, but FWIW most people (but not all!) put the saddle adjustment screws facing the pickups on T-O-M bridges.

Also, I agree with the others about the coolness of an explorer. I think everyone who has ever seen Eric Clapton playing it has wanted one at one time or another. Good choice! ;-) Also good choice on the black hardware. I usually prefer chrome, but somehow black just seems cool on explorers and T-birds and Firebird basses...