Are there any rules for controlling a vehicle remotely via the net? I haven't found any but it's a staple of the genre, in my opinion. Particularly coming at it from the angle of hacking in order to override controls.

I think a Comouters (Hacking) check should get you in. How easy that is depends on the vehicle or how the runner is doing the hack. Is it a pedestrian commuter hopper? Average difficulty to get in. An NAPD Detective personal Squadhop? Maybe hard or even Daunting.

Once in, I would ask that any check to remotely control it would be a Driving check that is decoupled to use Intelligence instead of Agility.

This sounds like a cool skill path.