ok from the xxxx manual models 1994-98 6cyl engines.

1/ Any time the battery is disconnected the transmission must re-learn the closed and wide-open throttle positions to enable the PCM to determine the proper gear to select for the appropriate throttle position. if the throttle calibration is not performed following power source interuption , the transmission will shift hard and perform poorly.

CALIBRATION
2/ Drive the vehicle until the engine is at normal operating temperature.
3/ Make sure the idle speed correct (approx 750 RPM)
4/ Set the closed throttle reference position by placing the transmission in "D", air conditioning off, and let the engine idle for 1min minimum.
5/ Next, set the wide-open throttle reference position by turning the engine off but leave the ignition switch ON (acc) then press the accelerator pedal to the floor and hold for 1min minimum.
6/ Place the gear selector in Park and switch off ignition. Drive the vehicle and check for proper shifting operation.


Another thing to check if gear changing is poor/irratic or in limp mode (3rd gear) is the gear position sensor ( large white assembly with 2 plugs on side of transmission), also the throttle position switch (on throttle body) if all is ok have a transmission centre do a diagnostic.