Hi, sorry to bump this thread, but I seem to have solved the problem on my end.
I decided to install mastercomfig for more fps, and followed his installation instructions which included cleaning out any custom cfgs and mods. I then installed his maxperformance cfg and the addons for badcpu, badgpu and ssd. The game launched in fullscreen mode, and to my surprise I had no more mouse delay with no strange fps cap, and the game felt much smoother as well.
I think it may have been the clean up part of the installation which solved the problem, but if not, try a preset or a combination of the addons.