A few things: 1.) When's the HDD last been defragmented? I believe Win7 has this enabled to run by default, but to check it go to Control Panel->System and Security->Administrative Tools. You can also adjust the time when the defrag runs. 2.)When does the choppiness seem to occur? Is it in games? A program? When? If it's just one thing, it might be due to that application, not a hardware issue. Track that down before you start swapping out anymore parts! 3.) CPU cooler. If the fan is loud, make sure it's not dusty. A can of compressed air can deal with this issue and run $5-10 most places. If that doesn't fix it, you'll need to look at the cooler itself and see if you can replace the fan. Depending on the cooler itself you may have to replace the entire thing. If not, you'll need to find out what size the fan is (e.g. 80mm, 120mm, etc) and pick up a new one. Should you go this route, I know Vantec used to make a Stealth line of fans designed to be quiet. Since CPU coolers do vary, I don't know what you have. Worst case scenario, take a picture and post it to this thread.
Can you please elaborate the stuttering sound cause its either a fan or a spark from a contact (highly unlikely) or could be a wire hitting a fan. I kinda doubt Ghostmans's suggestion of it being the motherboard but could be the hardrive ( but doubt that as well since all test showed up a clean result)
