I built up the sump today. I really didn't like the feel of the polyethylene tubing at the end of the caulking gun. However, I did get another suggestion on RC that I tried.
If your first run a bead of sealant along the line where you intend to mount your baffle, you can press the baffle against this bead, driving it into position and seal the back edge. The sealant is thick enough that you can then just run beads on the forward edge finishing the job. It works pretty well actually. It helps to mark the outside of the tank with a dry-erase marker to help direct you where to put the beads of sealant and to align the baffle.
As for cutting 1/4" plexiglas (which I was worried about), a cheap plywood saw blade mounted on a table saw (or a circular saw) works pretty well, though you will get some melting of the plastic saw dust as you cut. I used a smaller circular saw blade mounted on my 10" table saw and it worked just fine. Also, a plain-old jigsaw with a wood-cutting blade works well for shorter cuts and for notches. I do offer this advice, however: Especially when using a table saw, wear safety glasses and a long-sleeved shirt as there are little bits of hot plastic thrown off the blade while cutting the plexiglas. When it comes to cleanup, cut some scrap wood to help clean out the plastic residue from the saw blade gullets and, after removing the blade, use a razor to knock any plastic buildup off of the blade edge.