The CO adjustment is only there to make sure the cylinders are equal at idle. Not something you can do yourself without an EGA that can be hooked into the stock ports in the head pipes.

The larger speedstar manifold originally had to be paired with the larger speedstar injectors. The reason being that the pulse width range of the stock injectors wasn't enough for the increased air intake. It's possible that the stock injectors could be made to work by somehow increasing the available pressure. I'm not aware of anyone who offers a different pressure regulator. At closed loop cruise the stock system can probably handle things because the airflow won't be any different. It's during acceleration when the pulse width is hardwired according to throttle position that the increased airflow will cause a lean condition.

The difference in the speedstar injectors was that they delivered more fuel at a given pulse width than the stock injectors.

As I have stated before, and this is from the Yamaha FI manual, if the volumetric efficiency of the engine is changed the fuel delivery during open loop will remain the same.