Where are the Input and output speed sensors located and how to replace them?

They are both on the exterior of the transmission near the manual shift shaft. Both screw into the housing. To change them you unplug the electrical connector (be sure the seal for the connector comes out when removed) Then you unscrew them and screw in the replacements. Tighten to 20 ft lb. Reconnect the wiring and you are done. What is the issue you are having?