"Emulate 3 Button Mouse" limits functionality of shortcuts

Howdy all, first time posting.

I’m using a Wacom Bamboo tablet for Blender and selected “Emulate 3 Button Mouse” so that I can zoom and pan.
However, when it’s selected I lose some of the functionality of the the Control button, disallowing me to use shortcuts.

Will I have to remap the shortcuts to something such as the Command or Shift buttons? I want to do as little destruction to pre-set shortcuts as possible.
If I do have to re-write the shortcuts, are there any available scripts that I can use to batch process them?

Thank you for reading my question.