Excellent post. Really, really good. I have been following this case for years --- it is the case I find most perplexing and that I most want to see solved --- and somehow you've managed to speak more clearly about it than almost anyone I've ever read or listened to. Bravo.
Further, while I have long been suspicious of Karena for a variety of reasons, I can't really argue against what you have said above. And the list of scenarios you lay out as the remaining possibilities --- a stalker with an obsession, someone with a vendetta against Karena (and a case of mistaken identity), a neighbor who had been watching the girls for some time (more or less the first scenario) or a sexual predator --- is a very good one.
The thing that has never made sense to me about any of the above, however, is the time window. Karena left the apartment at 4:30am. How likely is it that any of the above would be entering the apartment intent on evil sometime between 4:30am and 7:00am or so? That time window just seems too late to me. I wish I could explain this better, but I just find that time window an unlikely one.
However, a thought just occurred to me which I haven't really ever considered before, and that is this: what if it wasn't a late night assault as it were but a morning assault? That is, what if this perpetrator awoke that morning with evil intentions, what if he had been fixating on the two girls, and what if he decided to see if he could get into their apartment that morning? Well, that's possible, except that there's one important thing against this theory, and that's the fact that he would have had reason to assume that both girls were in the apartment, and that should have kept him from carrying out an assault at that time.
And that takes me back to an idea I've expressed before, namely that it must be the case that the perpetrator somehow knew Faith was alone. And I can only think of one way he'd know that, and that's if he saw Karena leave. So that actually brings me back to it being a "late night" assault, i.e., he entered the apartment at 4:3oam, just after Karena left.
You are absolutely right that the police should have done better investigative work at the time, because the perpetrator absolutely had to be living in that apartment complex (in one way or another) at that time. I don't see any other possibility.