I'm looking for advice on bonding and bond-strengthening plywood box
structures (Marcos, for example, used spruce reinforcements at all
joints), and what thickness and kind of ply (Marcos used marine).

When I built my airplane I used plywood for many bulkheads about 14
years ago.
I got a good booklet on wooden boat building written by West Systems
Epoxy.
The epoxy is sold by West Marine nationally.

Here is an online link:

http://www.westsystem.com/webpages/userinfo/manual/

Good luck,