I'm not sure how much heat will help with silicone, since a lot of silicone stuff are used in high-temp applications. although, I haven't tried it, so I can't say it won't work.
Id avoid boiling water, there is too much of a chance of cracking the tank due to thermal stresses, etc.
I've bought ~ 80lb (I don't fish, but I find it pretty useful cordage for camping/etc.) in places like sports authority. Sometimes a walmart will have it, but it's pretty hit or miss.
Just to confirm, the overflow box itself is made of glass? And is it just siliconed on the back, or the back and the side.
How big is your tank?
Worst comes to worst, you may be able to break the overflow box, leaving just the rear panel attached, and cover the sharp edges with silicone