I don’t find the view3d.enable_manipulator, can you be more precise (I’m not so expert in blender customization)? I found only different options not related to manipulator.
I found a problem: you need to enable in User Preference File> Autorun Phyton Script, or scenes with Rigify cannot be open correctly.
Blender standard setting permitting to choice objects when you are in object or sculpt mode: press ALT+Leftmb and will appear a little menu with all the object under your mouse cursor, this option disappears with emulate 3 mouse button and even with your setting.
I found very useful the Wazou Pie Menu, thank to let me know that, previously I mapped right mouse button to Property panel, but now is really nasty and more useful. Not so useful the rmenu on middle mouse button (is a is a repetition of menu already present).
Also, why mapping 1,2,3, for view? I now used to piemenu now on Q key and vertex/face and edges on 1,2,3 keys. With your combo disappear a useful key combo: crtl+1 or 2 or 3 in edit mode autoactivate or cage subdivsion (crtl+1= subdivision at level 1, ctrl+2 subdivsion at level 2 etc), I guess you cage this because have just set this on some pie or menu, but going down or put off subdivsion (the not so friendly hotkey ctrl+0 combo) is nice to have.
I see you mapped left mouse selection timeline, I though was impossible to do…
I’ll continuing to test your setting. Not sure I’ll adopting it but for sure I extrapolate many nice things for my actual setting/workflow.