Things I would check.
- Wiring. Inspect the wiring coming out of the computer, check the ground wire that is located on the steering rod up by the hanble bars. Check all of the connectors. Light bulbs too.
The EFI systems have a Limp-Home mode. It is used if any of the sensors fail. This creates a over-rich condition and will greatly reduce preformance. However this system can also be activated if you have a loss in voltage. For example, pulling out your headlight and tail light will make the efi go in to the limp-home mode.
Check the LED light on the bottom of the EFI computer.
2. Water Temp
3. Air Intake
4. Not used in 98, barometer
5. injector failure.
Check sensors. Air intake sensor. Water temp sensor, Ignition Sensor. and the throttle postion sensor. The TPS is a potentiometer (voltage divider) and needs a special tool to calibrate. This ended up being my problem but I didn't have rich plugs, you do.
I doubt the problem is with the fuel pump. If anything it may be the presure regulator.
You mentioned water sensor fell off. The resistance should be 785ohms at .710 volts. (at operating temp 50c/122f).