Why chamber off 2-3" off the back of the entire tank and lose that much depth? If you want to chamber off an entire back section of a tank your best bet would just be going with a biocube. Honestly your easiest option thats really not that much more expensive is just to drill the tank and go with a sump. A sump will leave you with so many more skimmer and heater options just to name 2 of the endless possobilties running a sump.
Just so you know you can only drill a hole into the side panes of the tank. You can not drill the bottom pane it's tempered and will shatter.
You can assemble a glass overflow box but it'll be see through and most likely not perfectly square so if it were me I would go purchase a cheap retrofit black acrylic overflow box off of either bulkreefsupply or eBay. I got mine off eBay. Get building grade silicone not that crap marineland silicone in pet stores that's only meant for seam patch jobs. Marineland silicone will cause the overflow to tear right off the tank with a light tap say going to love something in he tank. The building grade silicone will create a seam so strong that you'll break the overflow box into pieces before it will detach itself from the glass. Many will tell you silicone will not bond to acrylic which is true silicone doesn't bond very well to acrylic. But I can guarantee none of them have used building grade silicone or even silicones acrylic to glass. I have installed 6 acrylic overflows to 6 different glass tanks with reef safe building grade silicone and guess what the 3 times I've had to remove the overflow box. The silicone I used which is reef safe has created a seal so strong and such a small gap between the acrylic and glass it has taken me no less the 40 min with brand new razor blades to get them off and have ended up scathing the tank because the silicone bond was so strong.
Sorry for the rant someone on here is gonna tell me not to do that, acrylic and silicone will fail but they have never used what I use or have never done it themselves. So point blank I'm going to tell you anyone that says otherwise is dead wrong. I will post the stuff I use and anyone that uses it with acrylic, attaches it's to a perfectly clean glass surface to bond to, gives it proper cure time and still has the guts to tell me not to silicone acrylic to glass. After trying to rip their overflow box off without breaking the overflow box or tank first cant come pick up my $10k+ 220g display, 400g total system volume for free.
Back to my original idea get a cheap black acrylic retrofit overflow box, building grade silicone, drill a hole in the back pane of glass for a 1" bulkhead with a appropriate size diamond glass hole bit (it's very simple to drill glass), get a 1" bulkhead, put the bulkhead into place either with the gasket although I prefer to remove the gasket and silicone the bulkhead into place with again building grade silicone, run a simple open siphon drain into a sump (another glass tank which will be DIY) then return the water via your return pump with a hang over the rim plastic return nozzle. Not that much more expensive then a biocube sectioned off back and gives you not only more space in your 40g but also so many more possibilities in regards to equipment and filtration.
You read so many words I most likely made it sounds like way more work and way harder then it really is to do so here's a picture of my 40g breeder. It's simple and it works. If your seriously thinking about doing it he way I did then I'll get you the link to the the over the rim return I used and the various black acrylic overflow options you have.
Entire view of my 40g breeder so you get a visual of how much of a minimal foot print the retrofit overflow box and over the rim return has.
Don't mind the hair algae. A close up of a CPR retrofit overflow box inside the tank.
Top view of the overflow. The best I could get without moving the light.
Inside the overflow with the bulkhead. Plumbing coming out of the bulkhead draining to the sump. You could use a different cap then I did and get the top of the drain below the rim of the tank.
Close up inside view of the hang over the edge return inside the tank.
Lastly the hang over the rim return outside the tank. This isn't the one in the previous picture I couldn't get a outside picture of that one so this is another one on a different tank. They are both the same returns. Except this one is 3/4" and the one on the 40g breeder is 1/2".
Your other option for the return of you don't want anything hanging over the rim. Which will be a tad more money would be another 1/2"-3/4" bulkhead drilled into the tank hard plumbed to the return with a loc-line spray nozzle inside the tank. Sorry for the long read but just trying to be as clear as possible and give you as many options as possible.
Link to the silicone I use.
http://www.ebay.com/itm/Silicone-Aq...hash=item3388239ad8:m:mKSOagyF_136dYxBYsqiI1g
