Cool deal.... As Al had suggested another bead of solvent?!?!? Could work, but you run a good chance of putting more stress on the joint than original and therefore it would be weaker than original.
I agree with your decision to cut the bottom off, and start with a bigger panel. I like to cut all my panels max 1/4 bigger than needed, except the height I cut dead on. With cutting your panels a little larger than designed it allows you to get the correct measurements of your project, and at the same time it allows you to make sure all your panels are perfectly square. The key is keeping it square, and no biggie if you have a little hangover on each side, because the flush cut router bit can be used to trim everything flush an clean. Thi is especially important when gluing the bottom panel to your walls.
I don't know what order your building your tank in, but your walls should be welded together, an then the bottom attached. This way the bottom can be adjusted if you were a little off somewhere instead of trying to tweak your side panels which would cause stress on your other panels. It also will allow you to take up any irregularities in any of the panels from bowing or what not. Again leaving a little hangover ensures you have complete coverage of material to glue to.
It looks from the pics you used a razor blade? I see a pretty consistent mark on the panels????? I would also advise that during construction to leave your panels covered with the protective sheeting. This helps prevent any undue scratching, splashes of glue and other mishaps. Just remove enough protective sheeting to properly glue the joint.
As far as prepping the edges as Al suggested either a jointed, or a router table. Another option is using a hand held router and you will need a straight edge to guide the router. As Al suggested you just want to remove a 1/32" or 1/16" tops. Even after I run it on the jointed or router I like to tape a piece of 220 sandpaper to my work table and slide the edge over the sandpaper. I tape it down so I know the acrylic is riding over a flat surface. It's to easy while hand sanding to round an edge over. After a couple passes on the 220 I tape a piece of 400 grit wet/dry paper am wet it down and again same procedure as before. I like my edges super smooth like glass. I then wipe my glue surfaces down to make sure they are clean and free of any junk. I use a quick swipe of alcohol, but I know Al disagrees with that practice. It had worked well for me, but on cheap extruded acrylic DON'T because it will craze and almost always will.
As far as taking the torch to the edge. Never torch or heat am edge to be glued before gluing. If you do you will not get a good, solid joint. If you browse Flowers thread you'll see the plastic framing squares I use and how I notched th out, which allows you to hold the panel in place, and at the same the same time you can at all times verify your panels are square. If the panels are super big or heavy another option is to clp the square to your work table to keep your panels square as you glue or double sided tape works quite well also. Another way is to build jigs out of 2x4's to square your panels. That is what I did for building my sump which in size is comparable to your frag tanks. These jigs now have doubled ad jigs to support my tank as I pour the epoxy for my tank. HTH a bit.....