Layer 3 Johnny being in a coma was tossed about in the plot threads. It's basically an explanation for layer 2 existing. Programming team finds a way to integrate thoughts into a virtual reality, programmer's son falls into coma, programmers attempt to prevent brain death by wiring son up to virtual reality. At first they don't think it's working, but eventually there start being subtle changes in the code. Glitches resolve themselves, and the characters seem more immersive. However, a virtual reality with potentially thousands of NPCs made finding Johnny very difficult, in fact it seemed like he might not exist. And then one day, they found a group of friends much more alive than the other AIs, and interacting with one of them in particular reminded the lead programmer of his son. Johnny layer 2 isn't johnny layer 3, but he's a kind of residual image. He doesn't have Johnny's memories, but he has some of his mannerisms and opinions. Basically every 'living' being in layer 2 is constructed from Johnny 3's psyche, while Johnny 2 is just the closest in personality form (they might not even share a name, and they probably don't look too similar).
As with all, this isn't certain and can be changed.
Kevin is the "cool" friend. Not the steriotypical jock, but like, he's the friend that always has the right thing to say and always seems to get his way in situations. He chose thief because that class gives him the most freedom in the game. He can go places others can't and can get stuff for free by using the steal ability. He shys away from any sort of talk regarding his dark past. This can only be revealed by favoring him over the others.
I like this, and I also like the idea that one of the layer 2 characters is actually a layer 3 avatar, but I don't think they should both be Kevin.
What if Eddy was the layer 3 avatar? Or another character?
If Eddy, then he is one of the people on the programming team, a tester of sorts. The Jessica arc (him helping her get out of the slums) is basically Eddy realising that they've made a virtual world and included suffering. He takes it into his own hands to try and ease the suffering that he feels guilty for. To guilt trip the lead programmers, he introduces Jessica and himself to Johnny and his friends. Once the programmers see Johnny's reaction to her upbringing, they agree with Eddy and, in an effort to alleviate the suffering of the virtual world, have a very rich family enter town, creating jobs, and generally raising everyone's standard of living. This family is retroactively made into Eddy's 'family' though he actually just unplugs himself from layer 2 whenever he goes home.
This also explains why Eddy didn't have the game, but doesn't explain why he would go to great lengths to obtain it even though the update is happening...
Oh good, we've reached the stage where our plot is complex enough that we have to worry about plot holes and continuity errors...
Purple scarf Rosetta is also my favorite, though I think (if possible) we should go for custom art. That is a nice template though.