[@Atrophy]
Alright good questions!

Question 1:
Okay I'm going to try and keep this as simple as possible in my explanation.  xD

The Net is split into two spaces, The Digital Sea and "Rooms". To think of the difference between them Digital Sea is like Tron and the Rooms are like the Matrix. Regular people can enter Rooms (They are a sort of odd conglomeration of apps and webpages) using something akin to a VR visor that can tap into the channel of a given Room. While the rooms themselves are akin to going to like a shopping website, but instead of it just being a website you would be transported to a giant room filled with endless shelves of items and such, or files and data would represent themselves as a room of endless filing cabinets or a library. In here people will do business, go shopping, and some rooms are designed specifically for pleasure simulations or relaxation. But yeah since all the rooms are corporate run and made they will be able to peak in on you and yes send you "subliminal messaging" to buy their products. xD The  Digital Sea on the other end is the sea of information between Rooms and extends as far as something like a computer or a phone is active. Sparks are special because they can enter Digital Spea for they possess special neural augmentations (otherwise your brain would fry up) and the training to not kill themselves. Because of this they can travel in the space between Rooms and jump between Rooms and access private rooms which would usually require some secure password or frequency to get inside. Sparks can follow the lines of communication between terminals, computers and cellphones and do so at astonishing speeds meaning that while usually a regular person will be constricted to the rooms in the broadcast range of their region, a Spark could hack into a Room on the other side of the world by sending their "virtual ghost" across the Digital Sea at the speed of light. It's because of this and how fast they travel and things operate that they find the real world so slow, because they can travel across the world in minutes while it takes a real person hours or days depending on method of travel.

But you are right in that Corps use Secure Intranets to prevent any old Spark to just wander inside and steal their data. Citadels as most Sparks will call Corporate System can only be accessed from secure terminals inside of the corporation requiring a Spark to infiltrate requiring other friends like Divers to back them up if they wanted to jack in. And Citadels will be composed of hundreds of different rooms with some being fake to throw a guy off or something like that.

And finally, normal people cannot be killed by rouge viruses or something like that, they will just be kicked from the system. Sparks will and that is because how their Neural Augs work basically when a virus or defense program attacks them what it is really doing is overloading their neural augs. If they get fried inside, well when input devices attached to brain either become super heated or explode? Well you usually don't come out alive and those that do are more or less mindless zombies.

Question 2:
In 2066 augmented individuals are a reality that everybody has to deal with and it shows accordingly in self defenses. For example most guns fire armor piercing rounds with generally more force and more punch to pierce through cybernetics or armored plating. Everything has become tiny antitank rifles of sorts and antitank rifles have just become bigger and scarier to tell with big and scary killer robots xD. But yes EMP grenades do exist and surprise surprise they actual work. But for the sake of balances purposes and since if EMPs could KO a cyborg in one shot augmentation companies would be out of business real quick, basically EMPs will take away the abilities of the Aug but not the functionality. So cybereyes will still work like eyes but they can no longer display information or see through walls and stuff, legs and arms will work like regular prosthetic legs and arms no longer able to jump higher or punch through walls and the like. 

Buuut Spooks being terrifying have two things they have special in their aresnal: "Pulse Tech Rifles" that when fired will shutdown all cybernetics completely in an individual making them limp, blind and easy to kill or whisk away, and they also have rudimentary EMP Shielding meaning that EMP grenades do not work on them.

Question #3

You know that would be a very interesting idea. I have no problem with him being an ex-Spook because being an outdated model, since it would mean he has none of their super OP shit that would make him into Death. xD And as an older model from a defunct company he would probably actually have his memories and something of a personality as well. Modern Spooks have routine memory wipes every six months taking away everything that isn't training or their instinct to kill and serve the Corp out of their head. Gotta keep your evil dogs of death on a leash right?