Passenger side blend motor just controls temperature on that side within a few degrees of the drivers side, I think, from memory there is about a 6deg. allowable difference from the drivers side which is the "Master" setting. If you have spliced the new motor(s) into the existing loom using soldered/heat shrink joints that should be ok as the motor loading is fairly low, current wise.
As has also been posted, a common cause of intermittent fault display can be down to low refridgerant level in the system, get the level/pressures checked by an aircon specialist...Kwik Fit have been mentioned on here as a good,reasonably priced source.
Have a read through RAVE>Blend Motor replacement and you will see the requirement for re-calibration. Another advantage is that at the same time as calibration is carried out, the HEVAC faults can be read and cleared plus any "Hard" faults identified.