Hello!
As far as I know:
Type 5 Prosthesis bonuses only affect that particular limb.
Implanted arms and legs..... GM call, or you could post a rules question. I assume yes, myself, for my games.
Type 3/4/5 are connected to your nervous system, hence the Surgery skill of 5+ and full hospital requirements. While they can be removed, some parts still remain in the person. Type 3 and 4 are bionic limbs and have increasingly effective abilities - GM's call on sense of touch, but feedback of some kind is required for people to have functionality. Type 5 is as close to human as you can get mechanically, and have enough of a seance of touch that the person wearing it takes Fatigue damage if it gets hit. No mention if they can turn off these senses, but I don't allow it in my games.
Running is less stressful with implanted feet (half fatigue). In terms of leg implants or prosthetics there's no mentioned in game effect so GM call. I say no to this in my games, just to keep it simple.
The weight of implants does increase the body weight of a character as it's added stuff. How much is GM call (from negligible to lots) I tend to ignore it. For prosthesis, They are probably comparable to the natural limb, maybe a bit heavier for type 3 or 4.
Hope that helps!
- Shane