Getting your body to work. (Mechanics)
Viral is a game of incredibly simple mechanics, or at least I think so. One system rules everything and it should only take a game or so to learn this system.
1. Identify what is you want your character to do. Decide which skill of yours it best fits under.
2. If the action isn't perfectly suited to the skill you have a -2 modifier. If you have no skill whatsoever for the skill you get a hefty -4 modifier.
3. Work out your total modifier using the below fomulae.
Skill level - ability negetives - skill representability (see step 2) -/+ un/favourable circumstances = Roll Modifier
4. Roll the die of the Aptitude that your skill falls under, then take away or add the modifier.
5. Check you result against the difficulty your GM gave you. Higher or equal is a success, lower is a failure. Don't worry too much about crap rolls, every one will be getting them.
Action difficulties.
Like grenading monkeys in a barrel: 2
Like shooting fish in a barrel: 4
Easy task: 5
Moderate task: 6
Challenging task: 7
Difficult: 8
Eep: 10
Simply the best!: 12
Example of a skill use.
Jim: Okay John, Amelia has sustained some damage to her cybernetic arm, your the only one around and it needs to be repaired now, otherwise it will be completly useless until you get it workshopped.
John: That's alright, I've got Cybernetic Crafting skill at 5 and I'm operating at only -2 intelligence and a medical Apt of D10. Thats a D10+3, right?
Jim: I'm afraid not, your skill only gives you a little knowledge about the actual technicalities of your arm, so you get a -2, also your operating on yourself, so thats another -2. Your currently on -1 to your roll.
John: D10-1 is still pretty good, I could pull of a difficult task.
Jim: Well I'm afraid your only going to be rolling D8, because your repairing it, not grafting it. So it's more of a technical roll than a medical roll.
John: Crap.
Jim: Right I'm going to be nice to you, I mean you really love that arm. It's only a moderate task, just a matter of swapping two cables around. Get a score of 7 and your fine.
John rolls and gets a seven, but with his -1 modifier that is a failure.
Jim: Goddamn it John! The red wire goes into the electropulse generator and the green into the nervous system translator, not the otherway round! When you try and move it there is a loud bang and a puff of smoke. You've now got a very heavy and useless chunk of metal hanging from you. -1 to any manual rolls to you get it repaired.
John cries.

Apt skill and phrasology (Insert esoteric unfunny leet joke)
My net access has been rather intermittent, so sorry if I haven't been too helpful lately. hopefully, I'll be able to catch up on my back-log of comments soon.
Anyway - I think it would be to your advantage to have a list of skills to be expected. Its rather difficult to first have free form skills for the players to make up, and then have criteria for what is or isn't appropriate. For that matter, I think the GM in the above example is being a bit of a bastard. Grafting cybernetics or getting at embedded ones would be surgery of some sort, basic mechanics would be electrical/mechanical engineering or a skill specific to prosthetics. I would have allowed no penalty in the above example.
On a related note, it might be easier in describing attributes from the start to explain: They all begin at 0 (or -1) and then you subtract a die roll based on your profession. Now, note the modifications inflicted by the viruses running through your system. The new, lower total is you normal attributes without enhancement packs. Next, assign your aptitudes - what kind of a die you roll for a task. Lastly, note skill levels.
A check is Skill level +/- attribute +/- penalties +a die roll.
"skill representability" might be better phrased as "No penalty for just the right skill, -2 for an applicable bit of knowledge, or -4 if completely clueless."
There is a fine line between hobby and obsession. I seem to have lost sight of it some time ago.