The unit is fitted and everything returned back to factory then the tuner will spend the next hour or 2 setting up how much fuel each of the injectors puts into the engine at set intervals of engine revs 250rpm at a time and also at different throttle positions.very interesting process and well worth it
I had mine done in March and it's made a massive difference to the bike so much more responsive at all revs in all gears! There are other options of plug and play chips which will work to a point but every engine is different so the only real true way of setting an engine is on the rollers!
PC's are pretty basic they control the amount of fuel going into each cylinder depending on the position of the throttle.
So having them balanced won't really make a difference as the only information the PC takes in is from the TPS.
It doesn't have sensors from the air coming in or anything to do with the timing, so before or after it won't make that much difference.