The operation of the NJIT/Rutgers FIR FEL is simulated for the first time sing the slightly modified UH code. The lasering behavior is explored for a wide range of parameters. Particularly, we studied the effects on the operation of the microtron based FEL due to the electron beam pulse phase instability which is possibly caused by the microtron cathode back heating. The study shows that for a small phase slew, systematic or random, there is little effect on the normal operation of the FEL. However, a dramatic phase slew of the e-pulse lasting for 1μs kills the operation of the FEL. We estimated the tolerance of the phase instability and discussed the proper operation condition of the device.