I had a similar issue. Part of the problem was the mice I had on hand to try. They didn't have great sensors, high polling rates, or they had snapping/correction built in to assist with drawing lines. Got a mouse with a known good sensor, the Deathadder, installed the Synapse software, and upped the polling rate. I also personally prefer setting the DPI to 4800 and turning the Windows sensitivity down. I know many will claim that's wrong, but it simply feels best/smoothest to me subjectively. Either way, this helped a lot with mouse movement.
I solved other microstutter issues by using D3DOverrider to force v-sync and triple buffering. I have the same options enabled in my GPU settings. And I enable the settings in games too. I know, redundant and silly, but it works for me. Sometimes this requires a bit of tweaking depending on the game, but that's just a matter of figuring out what settings work well together and maybe adjusting an ini file a bit. There are also some games that have issues with stuttering no matter what, including TES/Fallout games from Bethesda, and sometimes you can find user mods and tweaks to alleviate this.
In a nutshell, I basically require a nice, smooth mouse with a perfect sensor and a high polling rate in combination with every single game running v-sync and triple buffering if at all possible. The stuttering and tearing just kill me otherwise.
Best of luck in troubleshooting! I hope it's not some weird underlying issue, especially hardware.