2) -3 or so, I'd imagine. It's not quite as hard as shooting an eyeball, but, it's still not an easy target.
3) I'd say almost completely immobilizing, for the purposes of combat. It's really hard to walk with 15-20 pounds(that's being conservative) of dead chrome on your leg, let alone the outright pain and such of walking on an ankle. Atop all that, it doesn't just turn 'off.' A called shot to the foot would likely mangle it to Hell and back, tear it apart, and leave you dragging a whole bunch of pneumatic components and wires about. In the absolute least, I'd impose a -4 penalty on tests requiring the wounded foot or -2 and call a balance check on the player every time they did something. Getting 'shot in the foot' is still pretty damn lethal.
That said, I also run pretty lethal games.
I would be absolutely terrified of running in a game of yours... It's only a -3 penalty to completely annihilate a character? In that case, I'd just constantly aim at peoples feet...

Seriously, though, scary.
Falconer, your stuff makes sense to me, but still scary. For my own character as an example, he has a cyber arm(+2 armor, 9 body) and 18/18 armor. If someone wanted to shoot it, they'd roll their attack(-2 for aiming at the arm, -18 to bypass armor). Ok, it's an impossible shot. So they skip trying to bypass armor. They roll their 20 assault(-2 for aiming at the arm) vs my 5 REA. That's 6 hits, I make 2 saves. So they do 6 DV +4 net hits, -1 AP. That's 10 DV vs my BOD + Armor (9+21), so on average I'd reduce it by 10. Ok, so I'm safe, but assume I rolled poorly. I only reduced it by 6. So the arm takes 4 boxes of damage(it has 12 total), and I roll willpower(5) to save against 2S... right?