Pretty nifty there John!

If this is a knee tube and fully inside the cockpit, you shouldn't have any issues with the lid staying put, unless there is a chance of a surf bail out with the potential for waves to inundate your boat. The idea of putting a good bungie or velcro would then seem a good solution.

Try a sealant like 3M 5200, or cheaper/faster, Marine Goop (available everywhere--wally world, HD, lowes, Ace) to seal the plastic box inside the wooden box. Can't tell from the photo, but it looks like maybe you've just cut the bottom off the container rather than at the flange, and I think that's a good idea, leave as much "vertical flange" as you can for the sealant.

I'd shy away from the contact cement and sillycone. Don't know what contact cement you're using, I used the yellow DAP stuff to glue my foam seat and backrest in, and it works alright, but I've had to re-glue some also. It's water resistant, but sometimes lets go. If you're stashing ~$500 worth of electronics inside, I'd probably still consider putting them in heavy ziplocs or a little dry bag. Water's some wet stuff.

Here's an idea for a mod--is there a pelican box you can cut the bottom out of and use in the same way? The o-ring and latches are proven watertight, and you could score the plastic body real good, use some epoxy and get a real watertight seal with some good sealant up towards the lid/flange. If you haven't epoxied the stripped box yet, you could probably still modify that to fit.

Looks neat, please post further progress/testing results.