The '98 shop manual doesn't specify an amount of time the battery needs to be disconnected to "reset" it, but a couple of hours should be fine. Reconnect APPS, batteries, and turn the key to "on" (NOT "accessory") and SLOWLY press the pedal smoothly -- without stopping -- to the floor, hold it there for a brief second, then let it up slowly and smoothly again. All done. Ready to go. If it seems quirky or jerky or anything, ensure connections are clean and good and repeat the procedure.
Be careful taking the black plastic cover off the APPS housing/VP44. The fasteners are black plastic phillips and easily are broken... . i speak from experience.
New APPS is smooth as silk.
Tim