I have a 1999 5-speed. 2500~3000 RPM is a good shift point for the first two gears. The shift points in the Owner's Manual are fairly reasonable(24 km/h or 15 mph for 1-2, and 40 km/h or 25 mph for 2-3), so you can just use those. As for the third gear, that's very odd. Mine goes to ~1800 RPM @40 km/h(25 mph) in 3rd, so that's a very healthy RPM.
I would suspect the throttle body. Maybe try revving it in neutral and see if anything is funny.