If you block the mouse and keyboard of the quadstick with HIDHide, you won't be able to use them in mode 1.
I think the easiest way to deal with this problem is to split the config file into two separate files, one for mode 1 and a second file for modes 2 and 3, and run that second file in XBox 360 for PC mode. There will not be any mouse or keyboard connected to cause trouble.
Close QMP so there is no virtual XBox controller active when using XBox 360 for PC USB mode. I would also disable HIDHide, or even uninstall it.
It will take longer to switch between the KBM and Controller modes, but they will not interfere with each other.