To bond acrylic to acrylic, you will need weld-on. Nothing else will work. To bond acrylic to glass, you have to use silicon (GE#1 silicon available at Lowes will work fine.) As a matter of fact, I've read on here that AGA uses repackaged GE #1 silicon in their tank builds. Your best option would be to use all of one, or another for the overflow box (i.e. use glass to build the box, or use a hang in the tank overflow box like the one on the 90 gallon tank upstairs that I showed you.) To have an acrylic box hanging on a glass tank by silicon seals is a recipe for disaster. It not only stands a better chance of leaking, but also of just falling off completely.
As for the baffles, just silicon them in place using GE#1 silicon to the glass sides. seal the leading and trailing edges and they'll hold and be water tight. Silicon DOES bond to acrylic very lightly, but will peel off very easily if allowed to. Baffles experience very little forces that would cause the silicon to fail, so it works a lot better that way. Even overflow boxes are held to the glass mostly by water pressure into the corner of the tank. The silicon seals well to the glass too, which also keeps them there, but you should never think that your overflow boxes in the tank will remain sealed for the entire length of the tank. They might, but its far from a sure thing.