Noisy? Not really, though the stock fan in my system (i5-2400, same stock fan) was a bit "buzzy" for my tastes, due to the small size of the fan. It all comes down to personal sensitivity to that sort of thing, as well as case design. If you're at all concerned with DIY stuff, I'd say just get another cooler, they don't have to be super expensive, and the cost will be a lot less than jury rigging a cooler to your mobo and causing problems. You run into either damaging the mobo itself, or cooking the processor if you don't get a good seat, or your DIY solution lets go on you.
Corsair Vengeance is notorious for clearance problems with aftermarket cooling solutions, because of it's height. That problem will of course vary between coolers, so you should do some research on whatever cooler setup you choose.