people say to "degrease" your glass with turpentine to remove fingerprints, which I never understood, since turpentine is grease based.
I know this from my lithography (printmaking) experience. I'd say when you're using turpentine,
make sure you're wearing a respirator with properly stored organic filters, and follow it with a wiping of rubbing alcohol.
The turpentine leaves an oily residue, and the rubbing alcohol will make it squeeky clean afterwards. Basically they're solvents for two different things, and using both will make the glass super clean to work with. Rubbing alcohol's cheap anyways, so it doesn't hurt to use it.
Just make sure you're wearing new rubber gloves while handling the glass afterwards. Don't want to go through all the effort cleaning it only to muck it up again
Oh and don't be cheap when applying the silicone. Allow a 1mm thickness of silicone between the two glass panels. Apply masking tape before you silicone to get a clean edge. Just remember to remove the tape before the silicone dries. And if you get sloppy and get silicone somewhere that you don't want it, don't clean it while it's wet. Wait for it to dry and it'll come off real easy with a razor blade.
As for strongest silicone, I think GE 1200 would be just fine for a tank that size if you properly degrease it before-hand.
Big al's might have quoted you that price because getting polished glass isn't cheap usually. They charge by the inch to polish the glass to that nice smooth edge we all like. With a tank of the 40g size, you might be able to build it with acrylic for cheaper. You'd be dealing with a completely different set of problems if you did though.