That's basically right, except the judge did not grant the motion to dismiss because he had no power to. It was a recommendation that the Motion to Dismiss be granted, but the judge who wrote it was not the judge assigned to the case, so that would not have been binding. The USA itself would later file a different motion as to dismissing that count (as well as count two against Kane) and then sometime later dismiss count 1 against both.
What probably happened as to counts two and three was that the judge indicated to them that those counts would be dismissed, unless the USA wanted to just go ahead and dismiss them themselves. The USA wrote the Order to dismiss, which is actually somewhat common. An attorney for either party often writes an order as long as it is not one that is detrimental to the other party and the judge just reads and signs it. Sometimes a judge will directly tell an attorney to do this.
But, this is even more damning as to whether or not a crime was committed because, as to counts two and three, it was ultimately the prosecution to decide that no crime was committed...at least not under the counts they brought. They could have theoretically filed a Motion to Modify the original complaint to add new counts, but they never did, probably because they didn't think there were any other laws that had even conceivably been broken.
As far as Kane and Nestor, they were in state custody at the time the feds got to them, but it does not appear that any states pursued charges after the federal dismissal.