I don't think that the Dura Ace crankset used a taper that was anything different than the rest of the Shimano line-up. In fact, as far as I remember, there are only two tapers, ISO and JIS, and Shimano has always been JIS.

That being said, I've played fast and loose, put an ISO crank on a JIS taper and suffered no consequences at all. I know I'm not the only person to have done this; in fact I'm fairly sure Sheldon Brown even reported success himself.

More likely, you didn't tighten down your crank bolts enough and they just came loose. The taper could be messed up, but you might be able to make due by just really tightening them down something fierce. Use a torque wrench this time so you know what's enough, and then maybe exceed it by just a little.

And there is nothing you can do that will mess up the taper on your bottom bracket. Well, ok, there are things, but nothing that doesn't require extraordinary effort. Your Phil is safe, and will be for years to come.