The RC valve is controlled 3D by both PGMIII & IV. But there are still gains to be made by opening and closing at different rpm values.
The air solenoids bleed air into the emulsion tubes at specific rpm and throttle position.
As to whether the air solenoids are absolutely necessary or not would be a good discussion point. The F3 & NF5 don't have them so why would the NSR need them? However, they do add another variable to help tune the jetting at various rpm points, which is probably a good thing for a street bike that's used through it's full rpm range.
Yamaha use them on the 3MA & 3XV to pass emissions (as far as the info I got says).
To measure the ignition timing, RC valve timing, solenoid timing you need to build some test equipment and then map it all. My test stuff is mechanical as I'm not an electronics whizz. I have a box that mimics the flywheel, controlled by a fan motor. I built a motor speed controller using a schematic found on the net so I can adjust flywheel speeds from about 500rpm up to 13,000rpm. This uses NSR pickups which then just plug directly into the NSR harness.
It works pretty well. Had a bit of a scare with the first flywheel box I made. It was a shade out of balance and exploded @ 12,000rpm