This was posted at Motorcycle Consumer News at the time, and is a pretty fair description of what most likely happened:
Actually this guy has been posting on sportbikes.net and he said that he was riding a Honda RC51 with an aftermarket muffler, otherwise it's stock. That bike is by no stretch of the imagination capable of 200mph. Apparently the cop was in a plane using a stopwatch and was timing 2 bikes going different speeds with 2 stopwatches at the same time. He was timing them from hash mark to hash mark a 1/4 mile apart. Apparently the cops were patroling the area they knew a bike ride was occuring on.
More here http://www.mcnews.com/anforum/topic.asp?TOPIC_ID=61533&whichpage=1
IIRC, the factory HRC RC51s raced by Miguel DuHamel and Nicky Hayden just a few years ago, wouldn't quite hit 200MPH. Those were hand built, "factory" racers, that would have had a price tag somewhere near $200,000 to buy (which you couldn't... Honda only leases their racers to the satellite teams, and Miguel and Nicky were riding for the Honda factory).
Mark