I recently put together my first machine and so far its been great, except for a few issues. I've had numerous problems with my hdd like 100% disk usage causing the computer to freeze and having to constantly validate steam cache files. I defragged it and it has cut down on these problem almost completely. Recently though, every once in a while during a long session of using the pc, whether I'm watching a video, using video editing software, or playing a game, for a few seconds the video will stutter and the audio will make what I can only describe as sort of a "scrubbing". It only lasts a few seconds, and only happens maybe once a day, but it worries me. I put this under the Hard drive category because I really have no idea where this is coming from, but the hdd has been the only thing to give me problems so that's my best guess.
Try using another HDD. My friend had a new system built and he had (maybe a) similar stuttering issues. He would be on the desktop or watching something then it would randomly stutter. It turned out that the RAM sticks were glitchy but a 'further investigation' showed that also the video card was also a bit glitchy