The D5/MCP655 is native 1/2"ID...why not just use 1/2"ID tubing and fittings for your entire loop? This is a better solution than using those 3/8"-1/2" reducers that come in that package...just makes things more difficult than they really need to be.
The next problem is my AMD RADEON HD6990 (using XSPC razor waterblock) is having a very strange temp...its gpu1 and gpu2 has around 10-14 degrees differences (the gpu 1 is always hotter)...should I worry about it ?
This shouldn't happen. I run SLI GTX 560 Ti's in my loop, and they are always within about 1C of one another. I am guessing that the GPU block isn't seated correctly? Watercooling should keep these temps very, very close to one another.