If your going to water cool it then all of your performance increases will come in the form of lower temperatures. This will allow you to OC your GPU and CPU more. So what I would do is to benchmark your CPU and GPU in as high a clock speed that your comfortable (whatever max temp you are willing to get it up to) and record the results. After you've done the water cool mod I would OC until you've either gotten to your previous temps or have maxed out the clock speed. Then do a benchmark. The main difference you will see is the temperatures though.
Thanks I ended up using your suggestion with some additions.You can use HWiNFO to monitor temps before and after modification to see if your project has improved the cooling. You could run some before and after benchmarks too such as 3dmark11/vantage etc to see if the project keeps the system sufficiently cool under load.