Robert: I agree that it's a touch optimization problem. It's certainly not linear once we start considering distributions. Which is why I've been leaning away from an automatic solver like a linear optimizer but rather visual aids. That will keep the human element in the loop (and also make the problem tractable for us). But it also means that we won't be coming up with closed-form solutions and I don't think we'll ever be confident that our strategy is optimal in any kind of formal sense.
As far as your points, 1-3 are fairly easy--I just posted correlation matrices in the probability-distribution thread. Of course it would be nice to be able to vary them by specific pairs of players but for now I think correlation by position will get us pretty far. As for 1, I haven't done that, but it doesn't seem like that hard a problem, at least for a rough estimate.
Traditional portfolio theory won't work, for the reasons you mentioned but also because we're not trying to maximize total fantasy-points but rather the payouts from our lineups. That nonlinearity in there is killer. Still, I think some of the insights from portfolio theory are applicable in a general sense.