Ok, so a clean install of X-Plane, and the TBM, the stutters disappear.
Now it goes into the territory of extra plugins that are installed (These will chew up CPU cycles) or ortho scenery (this will tax your GPU).
Try installing plugins first, and see if the stutters re-occur. Best option is to install them one at a time, and starting X-Plane each time. This way, you can see which one, specifically, is causing the problem.