frequency the Nios II processor can support is roughtly from 20 to 120MHz

Be very careful how you implement the clock switching. If you are dynamically switching the clock speed without putting the processor into a reset state then the pipeline and other surrounding logic may become unstable causing the processor to go into the weeds. Normally what I see others do is store off the processor state into a memory that will stay live, force the processor into reset, switch the clocks, bring the processor out of reset, the processor executes code that restores the state.