I don't think you need the extra magnet volume, especially if they won't easily fit.
A bit of skew certainly won't hurt.
36 neos : 36 slots is going to cog no matter what.
Could use 72 square neos, something like Spdlmt150 except 2 in a row instead of 4,
http://fieldlines.com/board/index.php/topic,128761.0.htmlPlain epoxy is fine.
The "5 minute" stuff is NOT waterproof. Just resistant.
The slow cure stuff is waterproof.
Make sure the neos are clean of hand sweat, etc (i use 70% rubbing alcohol).
JBWeld is probably not a great idea for the first attempt. It is full of iron dust and it crawls all over the neos and makes a heck of a mess, which seems worse in small projects.
1/4x1/4 or 3/8x3/8 kind of leaves you guessing about the polarity. They stick together in more than one way.
I would suggest also getting a couple neo disks to use for a magnetic reference, and mark each neo with a perm marker on the side with the same polarity. It doesn't matter if you mark the N or S, but mark them all the same.
G-