Sorry I was thinking of a reg rubbermaid storage container.
Take a cardboard cut out to Home depot or lowes and let them do the acrylic cut out work for you for the stock tank. Test and epoxy it in
I buy liquid epoxy in bulk fro US composites so I couldn't really recomend a specific brand from the hardware store. They are all pretty much the same. Any clear two part liquid epoxy will probably work fine. The gel will probably have a better consistancy to work with.
On the size acrylic, if its going to depend on how big of stock tank along with how far the water levels will differ. I would probably lean toward the 3/8's though
Colin, what are you trying to baffle for? I used a 5 gallon bucket to run all my overflows into with a filter sock and have zero bubble issues if that's what you are doing. You could also use a smaller rubbermaid tub to do the same thing.
Colin if you do put in baffles and use the 2 part epoxy don't get the rapid like less than 5 min drying ones as you working time with it will be too short....I would get at lest 30 min or longer epoxy that way you will have plenty of working time.