The valves are connected to the servo cables. As long as the cables aren't broken, and the drive shaft not worn square, then the valve is moving with the servo. Pop the right fairing panel off and check...
Have you access to a dyno? If the bike is making more than 60hp then it's running fine and dandy - he's just got a better one!
Just a thought. What year is yours, and what year is his? Reason I ask is that in 1989 the NSR's got restricted, so if his is earlier, it'll be faster (I know you mentioned de-restricting, but it'll help to know the year all the same).
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