There’s a setting in SpecialK’s ReShade UI (Shift+F2 I believe is the default here instead of Shift+Home which it got changed to later for ReShade default bindings.) with some extra settings for SpecialK.
There’s one for drawing before the UI which works with a accompanying shader hash value, disabling that toggle can help but you do lose the ability to use SpecialK to draw shaders after the UI elements thus shaders won’t affect these.
Forgot the exact name here I think there’s two options in total as part of SpecialK ReShade D3D11 additions one might be on by default and then that works through a shaders ini file with the UI or HUD “hash” number selected which tells SpecialK and custom ReShade how to operate. 
EDIT: Hmm not that good at detailed explanations but opening ReShade and then in it’s UI the custom version here has an additional tab for SpecialK settings, toggle these and reload the preset and if that helps then for optimal functionality resolving the UI compatibility problem would be helpful as you would usually prefer not to affect UI text legibility and so on.
(I always had issues setting this up without custom ReShade no longer loading shaders at all but it’s been a long time since I used this so I do not remember the process in much detail.)
EDIT: Paths and such I believe are also hard-coded to .\Game Folder\ReShade\ for preferences and the shader files, possibly also paths for additional data like shader texture files but you would get a warning message (Red signifying something failed not the yellow text signifying some notification but nothing critical.)
Just from what I remember, probably already covered for but it’s been a long time since I used custom SpecialK ReShade so I only recall a couple of bits on how it was configured and what it needed if these extra bits were utilized. (Which are really handy but can take some configuring although FAR probably comes with much of that pre-set already in it’s default config files.)