To answer your original question about the Indian Tribe case... It was simply about whether the State of Florida could be sued in Federal Court under the legislation that required them to negotiate w/the tribes on gambling. Basically the 11th Amendment prohibits people from bringing a case against a state they are not a citizen of in federal court.
I'm unfamiliar with this issue, it seems like murky water. The federal courts have jurisdiction over a lot of things, but I know nothing about this. It seems like if a State is violating federal law they can be sued in federal court where the fed court has exclusive jurisdiction (meaning no other court may hear the case). The case, though, seems to have nothing to do with Raich or commerce clause jurisprudence.