The mechanism of the Morton Effect induced synchronous instability has been discussed in Part 1, using an assumption of isotropic linear bearings. The second part of the current study will now focus on the more realistic systems, mid-span rotors supported by the hydrodynamic journal bearings. First, the models to calculate the thermal bending of the shaft and the temperature distribution across the journal surface are established. This can be used to calculate the equivalent thermal imbalance. The calculations of the temperature difference and its equivalent thermal imbalance using hydrodynamic plain journal bearing models are conducted and discussed with the comparison to the analytical results obtained in Part 1. It shows that the thermal imbalance induced by the Morton Effect may increase to the level of the mechanical imbalance and then its influence on the system stability should be included. The suggested thermal bending model also partially explains that the mid-span rotors are less liable to be influenced by the Morton Effect induced instability than are the overhung configurations, because of the restraining effect between two supports. Finally, a symmetric mid-span rotor - hydrodynamic journal bearing system is calculated to show its stability performance. The results show the inclusion of the Morton Effect may lead to an unstable operation of the system. Considering the existence of the oil film self-induced vibration due to the dynamic characteristics of fluid film bearings, the Morton Effect may make a further negative impact on the stability of the system. The simulation results of the unbalance response show that the Morton Effect changes the shapes of the whirling orbits and makes them no longer the standard elliptical orbits around the static equilibriums.