I like the Klipsch Reference speakers, but the Klipsch subs are mediocre. Skip the Klipsch subwoofers. The new Hsu subs will be vastly better performers, I would for one of those, either the VTF3 mk5
or VTF15h mk2
With a good sub (or two), you will not need the low end extension of towers, so instead of tower speaker fronts, get bookshelf speakers. I would go for either RB-81s or RB-61s. Also, I would not go for the bipole Klipsch speakers, they will just mess up the surround sound stage. Substitute the RS-52s with another pair of RB-61s. It will sound better and be slightly cheaper. You could also step down to RB-51s for both pairs of surrounds and not miss much.
I agree with Jaykey, look for a deal on the Denon AVR-X4000 at the moment, that is a great AVR and is seeing some terrific discounts at the moment. It can independently calibrate two subwoofers separately and is probably the least expensive AVR able to do so. This is a very nice feature to have.
So a much better system for roughly the same price:
Klipsch RB-81s for front left/right
Klipsch RB-51s for side surround left/right and rear surround left/right.
Klipsch RC-62 center speaker
Hsu VTF3 mk5
All of that costs the same, $3500 shipped, and should be much better, thanks mainly to the substitution of the killer subwoofer. Acoustic Sound Design would probably be willing to give you a price break on the Klipsch speakers if you asked. They are willing to bargain, so you could save more money there. If you wanted to go the dual subwoofer route, Hsu is willing to give you discounts on multi sub purchases as well.
A couple more tips: for speaker cable, just use a roll of 14 AWG speaker cable from Home Depot. Do not buy speaker cable at electronics stores like Radio Shack and BestBuy, the markup is insane. For HDMI cable, just get it from monoprice.com
, as with speaker cable, the markups are crazy on HDMI cable. If you need bookshelf speaker mounts for the surrounds, the best affordable ones are the Videosecu side-clamping bookshelf speaker mounts