Hi Nathan,
+1 for loving the explorer shape, and my first build was an explorer.

Plus from Drashkum's post:

1. I would wind the high e saddle forwards a bit and the low E back a bit, and make sure that 628 mm can be achieved with the high e and about 632 for the low E, and still have room for more adjustments if needed.

2. ?? I'm not sure if that is the norm. But glue should fill up the space.

3. The neck will not line up with the neck pup route. But, you need to ensure the neck pup (with the surround) will fit into the route cavity, and be flush with the end of the neck, and not leave any of the route recess visible.

I don't think there is normally much wiggle room but points 1 and 3 must work together.