According to the Haynes manual, the 2000 R1 got improved in the new silencer and remapped ignition+EXUP-valve+carburettors which led to a 7.9 bhp increase. Haynes also says that service intervalls are improved from 6000 km to 10000 km.
(And ofcourse, the new bodywork, fuel tank, strengthened frame, improved gearbox, modified springs front+rear, lighter break components front+rear.)
I do not know what Yamaha official figures are, but Haynes do say 140 bhp/[email protected] rpm for 98-99 year models and 147.9/[email protected] rpm for 2000. These figures are "Performance data sourced from Motor Cycle News road test features", http://www.motorcyclenews.com.
Measured in different ways? Perhaps meant to be 150 bhp for both? Tourque was 79 lbf ft/107 [email protected] rpm 98-99 and 79.5 lbf ft/108 [email protected] rpm. All these figures are actually within margins so that it can be individual differences and atmospherical conditions and so on.
...to add to the confusion.
The recalls on the 98 R1 were:
1. Clutch basket fractures around cush drive springs.
2. The glue that held the brake pad friction material to the backing plates could let go.
There never was a problem with second gear, at least not officially.
The problems with second gear is related to ham-fisted (ham-footed?) riding. Luckily it´s not too hard to fix yourself.