be careful with used window glass. . . the UV is really hard on glass and makes it quite brittle - if you are going to use any plywood, I would suggest building the box out of plywood and only having one side with glass. Silicone doesn't stick to wood or anything that you would put on the wood like it does to glass, it can create a pretty serious weakness in the joints. If you decide to go ahead with the tank, please keep us updated as to how you construct it, I love seeing how people do things differently and how they all seem to work out in the end.
Ray