To my knowledge the best thing you can do with an NSR in order to go fast is just to keep it as Honda as you can.. (forget about,RM pistons,whatever pistons or other ignitions etc) and most importand,keep it simple..
PGMIV is a really cool ignition,card programming,cool looking clocks with the LCD,unique steering lock etc etc but other than these feautures imho its a pain in the ass if you want to take the most out of a stock bike.