I am sorry, the QX9850 is not out yet, what i ment to type was the QX9650, but building a system like that I personally would be willing to wait a bit for the 9850 to come out.
The price is about 300 bucks more the the 9650vs6850, but from what I've read and having used the 9650 before It seems the way to go if money is not a factor.
I am curious why you chose the FX5500. Like Hyper_Shadow said it's not a great choice for gaming, but rather suited for graphic design and CAD,DCC apps.
I have installed a couple different brand water coolers, and yes they can be a lot of trouble sometimes. If your not going to OC then it should be just fine on air cooling though. You said your case has 1 120mm exhaust and 1 180mm intake, with up to 9 more 120mm fans? That's a lot of air movement.
I agree that a 1kw PSU is a lot of juice, but if you plan on running duel video cards, and fill all your bays, (and fan slots), then you know you will not run out of power. But you could get away with less like Hyper_Shadow said.
Good luck, and let us know what you end up with.
