Secondaries - Somewhere I read that it's better to leave them 100% open than remove them - UNLESS you also remove the bar they pivot on.
Gentlemen, the use of the secondary air blade and the low gear ignition retardation is primarily to meet emission requirements. However, as Dougl states, the ignition should be less advanced at lower rpm because the burn rate is nearly constant regardless of throttle position or engine rpm. But if it is retarded even further than needed to optimize combustion, the exhaust temperature rises and the cat's efficiency goes up. Keeping the cat hot at low speed is needed as engine load is low and exhaust temps drop. This is accomplished by adding fuel and retarding ignition and then burning that mixture in the cat. Sounds weird but it is true. Even though the combustion is dirtier, the tail pipe emissions are cleaner. Hint, hint!
The secondary plates are used just like the vacuum slide in a CV Mukini; air is metered closer to engine demand. Recall the old Triumph twins with Amals: twisting the throttle too far too quickly slowed you down. Minimizing lag was why accelerator pumps where invented. But dumping extra fuel in doesn't lend itself to mileage enhancement or reduced emissions. A secondary use is to reduce torque. A "designer" torque curve can be created. Torque peaks can be shaved off so that engine response is nearly linear across a wide rpm range.
Someone mentioned seeing what happens on a dyno. While I haven't dynoed that test directly, my Rocket has been dynoed on a steady state eddy-current dyno at 10, 20, 30, 40, 75 and 100% throttle openings from 1,400rpm at the lower throttle openings to 6,750rpm. With secondary plates in place but fully open, my bike, for example, makes as much torque at 2,300 rpm at 40% throttle as it does at 100% throttle. Why? Because the engine at 2,300 rpm needs only 34% of what it needs at 6,750 rpm at 100% volumetric efficiency. More throttle opening than needed to meet engine demand does nothing to increase power.
So the upshot of this is if the plates are removed or opened fully in the tune more fuel is needed to prevent throttle lag when accelerating. However, adding fuel in the fueling tables adds fuel all the time at that throttle position. We don't have access to transition fueling tables using TuneECU. So, most tunes for open secondaries have more fuel for throttle response but are too rich for steady state running. Compromises are always required.
As to if more air flows with the blades in place and open versus removed, probably not. The shaft is quite far from the lower primary blades and if I recall correctly in a slighter larger bore. And the blades are not thin nor knife edged to enhance air flow.
I have my plates set at reduced opening at 2,500 rpm and lower and run my tune a little leaner than most. I don't wheelie so this works for me.