Op you know what, you are getting good advice here. You seem to have made up your mind, so it's your money. Do what you want, but we told you so. I've worked on similar systems and came away not impressed at all.
I worked on one where the power supply needed replaced, as well as the video card. Replaced those. Then the water cooler was leaking, which leaked and fried the motherboard. I took care of that, but the water that leaked seemed to damaged the new video card (Radeon 7970 from microcenter), as it had issues also. Note I'd gotten a combo deal from microcenter for the new board and a new cpu, so back I went, changed it to a hyper 212 evo for air cooling, replaced the board yet again, replaced cpu for good measure, and new video card and power supply in case of any problems. The nicest thing about the ordeal was that with their return policy we didn't have extra cash out of pocket. If there was it was very little. We also got the 2 year warranty on the parts in case of issues. Since then, no calls about issues, so I'm assuming no news is good news.
Look at local pc shops and see what they would charge. That would be a far better option.
Do you have a microcenter near you? If so go in there, pick out the parts you want, their sales guys usually know their stuff. Pick out what you want in parts, and they offer to assemble it for 130 bucks. So then you'd still save money, and get a good system.
And no, I do not work for microcenter and am not affiliated with them. I just buy almost all my stuff there. The one near me has great customer service and price matches newegg and amazon I think as well. So if you are not comfortable building, that would be a good way to go. Also they will sell you 2 year replacement plans on individual parts, so you could but warranties on whatever you like and just a drive to the store if you do have trouble.