I have Mitsubishi plc, I need help for writing ladder logic for generating the clock pulse, amount of clock pulse, to set the frequency of clock pulse and to read the encoder details.

Any hands ???

I have exp with omron servo motors and controllers, but it should be standard mostly, you need to calculate the position or rotations you want to utilize to perform your task according to the pulses required per rotation for the motor and then convert the decimal value of pulses into long hex value. this value should be written to the data file position of the servo controller linked to the PLC. Before anything else you would need to get the electronic gear ratio from the papers of the servo motor,so that you can find the no. of pulses required to move a rotation.

You are unable to use the PLC:s internal clock pulses in your application (Appendix A-1, page 473 of the FX-series hardware manual)? If so, you may need a faster PLC.