Not much engine wise.
The problem that the '98 and '99 models had were the gearbox which failed to perform in 2nd gear.
Yamaha gave the service to fix this problem for free at any Yamaha dealer. Most R1's should be fixed.
Blue streak mentioned earlier that the '99 (I guess the '98 too becuase the have the same parts) are more wheelie prone.
Powerwise, there is no difference.
The problem that the '98 and '99 models had were the gearbox which failed to perform in 2nd gear.
Yamaha gave the service to fix this problem for free at any Yamaha dealer. Most R1's should be fixed.
Blue streak mentioned earlier that the '99 (I guess the '98 too becuase the have the same parts) are more wheelie prone.
Powerwise, there is no difference.