I have found that Helmsman Spar Varnish is a hard one to beat with clear silicone calking. Usually 3 coats will do it. I used to make wooden canoes in the 60's and we only had to refinish about every 10 years. So the Helmsman is some tough stuff.
I have made about 7 sluices so far and used that combination on them and they work well. I think you will enjoy building your own sluice and when you find out how easy it is, it probably won't be the last. I just finished up a small recirculating fluid bed sluice my self and it's surprising how much material you can run through these things before you have to clean out.