You will not be turning the mains at all. The adjusting you will do is to the air mixture screws.
The piots and main jets once installed are not turned or adjusted.
Yes, if I understand you correctly that is a good plan.
Remove the old pilot jet and install the new one. turn the air mixture screws out on each carb three turns and then go ride it and see how she runs. If the popping is greatly reduced or virtually gone other than some burbling on decel ....that is where you want to be.
I hope I am not misinterpreting you.
