If you did a factory reset Rusty you will have to go thu the dock side wizard first thing before moving the boat either setting still at the dock or on the trailer. It will walk you thu step by step what to do and how to make the changes to the drive polarity ( rudder/outboard in your case ) direction. If it is turning to starboard instead of port as you said it will ask yes or no. select no and it will do the test again and ask you yes or no again. If yes this time select yes, and your drive polarity is all set in the computer, then continue on with the wizard. On another note did you by chance put anything metal or move the electric trolling motor head ( I think you had a bow mount on it when I put it on ) closer to the EV1 ?
Sec 5 explains about the compass linearization being set automatically at power up, but can be fine tuned with sea trial. It has no bearing on the actual operation of the pilot itself.
Note that your system Does Not have a rudder reference so follow the set up accordingly