As I mentioned in my original post, I did not have the software fuse set on Fan 4 when I connected the Pump.
On a chance, I removed all power from the system (shut down power supply), and that did not restore Fan 2.
I changed the pump over to a Poweradjust Unit, and initially it worked. Then, while attempting to control the voltage to the pump things became erratic.
At this point, I decided to restore everything to factory defaults, and reload the Firmware on to the Aquaero 6. I also restored the PA and the MPS Flow Sensor.
Removed all power after the restorations, waited about 5 minutes, fired the Aquaero up with nothing attached. activated the fuses for Fans 1 - 4, and wala, Fan 2 output works.
I don't want to take a chance on restoring setting from my saved settings, so I'll reprogram and save as I go along.
Good to know that support was ready to step up and help though.
Thanks
RodeoGeorge