Dave:
When playing with your secondaries, and opening the throttle only partially/gradually, the secondaries won't open at 3500 RPM. They open that low when the throttle is open by a larger margin (ie aggressive driving). If you are only snapping the throttle up to 4000 RPM or so, then letting off, its normal for it to just open partially. You have to keep it spooling up longer to give them a chance to open fully (ie under load, while driving).
As for cracking your secondaries, you should find, on the lower intake manifold, a stopper adjustment screwfor the intake runners on the transmission side, alongside the linkage. You can turn it inso that the runners, when closed, will be left partially open.
I must inform you, before you do this, its a hit or miss mod. Some have had positive results from it,while others, like myself,actually hurt performance by doing this.