Tell me if this example is correct, and fill in what I leave out:

I have taken 3 Physical, 3 Stun, and 3 Matrix damage boxes.

Resisting damage: No wound penalty.
Shooting a gun: -2 wound penalty.
Shooting a gun (AR-assisted smartlink): ???
Driving a van manually: -2 wound penalty.
Driving a van (AR-assisted): ???
Rigging a van: -3 wound penalty.
Hacking a node: -3 wound penalty.

If I take High Pain Tolerance (R1) or a similar damage-box-ignoring ability, my real-world penalties (Stun and Physical) would be 0.
But does this quality affect my Matrix persona too?

Not at all, unless you're a TM, in which case your Matrix track IS you stun track.