Well it looks like I'm reviving this again lol. Different system specs for everything but the GPU and some storage now. If anyone stumbles upon this page from a google search and none of the suggestions from this thread have helped you, there is likely no fix. Your eyes are simply more sensitive. That's how it is for me.
There isn't a single electronic device on earth that plays games without stutter. There are some games which have, for all intents and purposes, no stutters. Capping the framerate also helps with smoothness considerably. However, those games are far and few between, with 99% of open world games stuttering. In those games, the stuttering happens since the game hangs while waiting on ressources from the hard drive. While it's possible to load ressources without halting the gameplay, not many developers go through the effort. There are other reasons, like shader compilation, which is also something that can be fixed by developers but that not many go through the effort. There's also the fact that computers make mistakes all the time, they're just very good at recovering from them. Then, there's the OS you're running on. Windows does a ton of stuff in the background. If you eliminate all the extra bloat and telemetry, a lot of your stutters will reduce in intensity and frequency. This also applies to any kind of running program other than the game you're playing. There are also hardware combinations that will produce more or less stutters. Of course, you may not have the leisure of testing all the possibilities. After all, no two components are exactly the same even if they share the same part number, manufacturer, etc.
What you can ultimately do, as a reasonable person with sensitive eyes is get a g-sync or freesync monitor, turn it on, cap your framerate to between the 1% lows and the minimum observable fps you get, and take the occasional stutter.
If you're a bit on the unreasonable side, and you've been tired of this for a long time, you may want to look into other things. Whether they will be of help will be for you to figure out. Things like adding a UPS that has a high-quality inverter in-between the wall and your system, using a power cord that is both bigger and contains more wires, using a power supply with excellent ripple characteristics, installing a stripped-down version of windows that contains none of the crap (that one alone helps a lot), limiting the number of programs that run in the background, getting the ultimate fastest storage device you can, fastest cpu, memory, everything, swapping parts one by one and benchmarking each to see which alleviate the stutters the most.
In the end, I don't think focusing on this too much will be of help to you, as it will leave you with an impossible problem to completely eradicate, mainly because there are external factors at play. As you can see, I started this thread in 2017 and we are now in 2022. I have continued searching for a way to fix stutters for a few years, testing many things and becoming a lot more knowledgeable when it comes to electronics overall. Now don't get me wrong, it's not worthless to look into this and try to improve the situation. Just be aware that it can't be fixed. If after reading all this, you think that there's something wrong with my PC, and for that matter all of the PC's I've tested (granted not that many), then you do not have eyes as sensitive as mine or as others who have this problem. Your system stutters, but you have the good fortune of not being able to see it, or the games you play happen to not be affected as much.