Try setting your refresh rate in the config to match your monitors which I am guessing is 120 Hz.
With my G-Sync setup disbaling V-Sync introduced that same stutter you described but setting my refresh rate in the config to 144 Hz solved it.
I agree with you about the Royale shaders (especially the Kurozumi version), they look great and of course shaders are all about personal preference. I just found the Aperture one to be a great all around balance of great looking and only a single pass so it's very light weight.
I'm really not a fan of no shaders at all though, the raw upscaled pixels to me look like absolute shit, just my opinion and preference though.