Hi Rich,
Well done on your choice of axe to build. I love mine- sounds fantastic and the action is awesome.
1st Question: - Totally up to you but be warned once the neck goes on it'll be quite heavy and long and difficult to manoeuvre when your trying to finish it. And if you plan on using a spray lacquer as your top coat then it'll be doubly hard to spray into the difficult to get to parts. Just my opinion. I joined my neck after all the finish was done and the neck join is fine by me.
2nd Question: Neck pocket on my esb4 was so tight that there was no movement to be had in any direction. I was lucky I guess that the fit was perfect and everything lined up as it should. Setup and intonation is perfect. The 3 point bridge has been an absolute nightmare. Bad design! I've ended up glueing in some toothpicks in the holes and the bridge has now been holding for a few weeks but this is my third attempt at a fix. I hope yours fairs better mate! My last resort will be a Hipshot but that'll be a ways off because they are pricey!
3rd Question: I taped the binding on the side profile and as Wokka said scrape or sand the stain off the top profile.

Good luck and ask any questions you need answered as you go!
It's an awesome guitar once all together. You'll love it!