Well, after rigging it that way, I find out the knee is supposed to bend as if it's built along the YZ plane. Naturally I can't just make a chain along the YZ plane because the joint pivots won't be in the locations they need to be in and the deforms will be horrible.
If I want to keep this rigged as IK, the only thing I've been able to come up with is to make another hip -> knee -> ankle chain built along the YZ plane, then IK that and write an expression to link the old chain with the new so that the leg deforms properly and points down the z-axis instead of the x-axis. The only problem with that, is I'm assuming I'm going to need some kind of offset for the two chains, which I haven't figured out yet.
So if anyone can come up with a solution, I'd love to hear it. Even if its just a "I think this might work, give it a shot and see" type of response.