So I'm trying a technique to waterproof the wood components of my new system expansion.

1. 100% clear silicone (smells like vinegar)
2. Citrus solvent. From orange peels (I got it from Real Milk Paint company), could also use mineral spirits if you don't mind the risk from the volatiles. They should evaporate out pretty fast IMO and not pose much of threat. I still used citrus solvent because I thought that would be totally safe.
3. Glass bowl to mix them in
4. Detail roller to apply

Put the solvent in the bowl and then a glob of silicone and mix them together for awhile. After about ten minutes of mixing the clumps of silicone will be pretty dissolved. Use the roller to apply onto un-finished wood. The solution soaks into the pores of the wood and repels water. A thin mixture soaks into the wood pores very well.

I have a trough I made with 2x4s and pond liner that has been sitting with water in it since January and the wood still doesn't show any water soaking into it. I initially tried two coats, thinner then thicker but it seems to work fine with just one thin coat. If you've ever tried to scrape silicone off a porous surface you'll know this won't go anywhere for a while.

HTH, have fun if you try it!