Aaron,
That is a lovely looking bass. And a nice truss rod cover too, which I think that deserves to be bolted on. What you want is the threaded inserts that Alembic use - same as what you should have for your rear panels. You could probably get a few inserts with their machine screw brothers from Mica. You could even get brass headed screws if you want a close match.
Adhesive foam or double sided tape would work but you do want to have access to make adjustments every now and then. And though Gary's magnet idea sounds very slick, there are two possible issues there. One is, the pickup is a powerful magnet so I'm not sure it would work to have another magnet inside the pickup's field. Though maybe you could rig it so that the cover is powerfully ejected simply by lowering the pickup until the two magnetic poles repel each other. Slick!! The other issue is of course vibration. Anything that isn't securely bolted down will find a way to rattle at a certain pitch and that physical rattle can be passed through the pickups in an unmusical way...
Jimmy J
