Great work! I just found your post as I was investigating battery solutions for the blaster. I tried 18650 cell and it fits well in the raise section and powers 3.3v arduino well. I was looking at using this, https://www.thingiverse.com/thing:2847497, before I saw your solution.
I like your idea of the endcap magnet to connect to the main blaster. One suggestion on the magnets/screws, if you use non-stainless screws, you can align the magnets to attach directly to the screws instead of having magnets on both sides.
Paint should cover the resin, might need a couple coats of black to remove the see through nature of the resin. I am using resin and tested with just adhesion promotor and 1 coat paint/clear and seemed good enough.
I am currently working on modifying E11 blaster electronics to add F11 sounds and options for light and stuff.