I would say the first time you clamp down the processor, I was fairly sure the noises it made meant I had shattered it to pieces lol. Fortunately no , second I would +1 installing the cooler.
the hardest part would have to be picking out the best parts for your budget. unless you stay current on parts it can be quite a big list of things to sort though.
the most worrisome part is clamping down a big cpu cooler. they are on there VERY tight. i remember the first time i put one on i thought i was going to break the board in half.
actually flat cables can work quite nicely if your case has grommets and you can route cables flat behind the motherboard tray. it all depends on your particular case and situation.