You didn't mention where you were riding, so if it is not in the UK, then low octane fuel could be the problem.
Assumedly if you did 400 miles, then you must have filled up your tank halfway through the ride? Did the power loss become noticeable after filling up the tank? If so, maybe it was dodgy fuel?
If you have a 2003 model, then the CDI should be switchable for low octane fuel. You could try switching the CDI to see if it runs better (assuming you still have the same tank of gas). There is a post in this section that shows how to disconnect the CDI switch for low octane (<95).
good luck
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