Several problems with SIP disabled?

After weeks of frustration I disabled SIP, to get TotalFinder back in the game. I couldn’t be without my double tap on Option to instantly get a (double) Finder Window. And to have folders on top.

But! After I disabled SIP my Logitech Unifying Mouse (Performance MX) is not working properly. I can’t use or configure any of the extra buttons. Same thing with my Logitech S 530 Mac keyboard (which is not Unifying though). My Canon scanner software (MP Navigator EX) crashes at start. Anyone who experienced similar problems? Is it because I disabled SIP or may there be another explanation?

Could you try to enable SIP fully and test it again with original settings?

I’m afraid nobody here will be able to help because you have quite unique setup.