Your project sounds like a lot of fun, with a lot of opportunities for us (and you) to learn along the way. If you don't have it already, there is a prior issue of PB Magazine that shows how to make the brook trout spawning box that you referenced. It is available from the PB Headquarters for a modest fee and is certainly worth the read.

I had the same question you have about the possibility of WE using it. This could be a good thing or a bad thing, depending on the goals of having WE to begin with. I'm curious to know if any of the experts here have an opinion on the topic.

Best of luck with your project. Please continue to share here so we can all learn as you go.