Fuel table adjustment

We are using a Link G4 storm on a motorcycle engine of our own construction. It is a twin cylinder with evenly spaced firing ie 360 degrees apart. Engine is 1200cc ,air cooled, and has a throttle body for each cylinder and so we are using TPS for load measurement. In step 7 you create a steady state fuel table using a flat ignition table of 15 degrees advance. In step 9 you do full power runs and make adjustments to ignition and fuel tables on full throttle only. Once the ignition table has been established as in step 8 is it necessary to do a second iteration of the steady state fuel table. I understand that altering the spark timing will not change the amount of air entering the cylinders but could later than optimal timing cause incomplete combustion and therefore give a false reading on the oxygen sensor. Also would the late timing cause the engine to run hot.

It's definitely worth revisiting the fuelling once you've got the timing optimised. As you've correctly noted, the spark won't affect the AFR, however sometimes with a knock prone engine we can use more timing if we richen the mixture which helps cool the combustion temp.