If he drilled the slide transfer ports and went to lighter springs and you are running pods then what you are seeing on the dyno sweep test at low RPM is the lean spike when the slide is opening too fast from a setup that isn't in proper balance.

Don't assume that the pilot is too small or the screw isn't properly set because the slide is raising too fast on a sweep test.

I've done a lot of spring testing & can prolly help you. In order to do that we'll need to know EXACTLY what the current situation is with the air port dimension, current vaccum spring, & needle.

See if you can get answers to the other questions & we'll go from there.

One thing is certain - your bike isn't optimally tuned, and it CAN be improved!