DrAwesome109 :
If you think you're going to spend less than $1000 watercooling, you've got another thing coming your way. You can't just buy a case that supports watercooling. Each piece of hardware you're trying to overclock will need a waterblock to replace whatever kind of heatsink is already on it. Taking the cooler of a 6990 will not only void the warranty, but it will be a huge pain and will greatly increase the probability of having to get another one.
Overclocking? Just buy decent parts now, then overclock in two or three years when Modern Warfare 6 comes out.
YES. I LOVE it when people who don't know what they're talking about just come over and start posting wrong information. *facepalm*
I built my loop (CPU + 2xGPUs, 2 rads) for about $600. $1000, and we'd be talking LN2 or phase-change.
I've seen hybrid loops (albeit, doesn't make too much sense) where the CPU was aircooled and the GPUs were watercooled, and all components were OCed. Some CPUs don't benefit from watercooling, because they'll hit 4.7+ GHz on air with a $100 cooler, and 4.8 on water in a $600 loop. There are hybrid loops out there specifically because of this.
I assume you don't read your warranties at all based on your comments. Though EVGA doesn't make a 6990, I know for a fact that their warranty will cover their cards with aftermarket coolers:
From http://www.evga.com/support/warranty/
The product must be returned to EVGA in the original factory configuration and condition. All aftermarket modification must be reversed before sending in the product for replacement.
Some companies don't even cover OCs, but it all depends on the manufacturer's terms and conditions. I read all of mine so I know when I'm covered and when I'm not.
@OP - Besides picking the right blocks and rads, the biggest logistical challenge is figuring out where you are going to mount the radiators.
-Are you comfortable modding (i.e. drilling/cutting with something like a Dremel), because it generally requires at least some modification in even watercooling-ready cases (depends on brand and what you're doing).
-Do you care if the loop is all internal or if parts are external (latter has many more options - usually you can get bigger rads).