massive reconfiguration time again.
That link to the secondaries is 100% Holley. Just remove the link and wire the secondaries shut. I've seen guys not do that and the secondaries open and then don't shut. That will fill your shorts right quick.
I think you're on the right track. Get the primaries divorced from the secondaries and tune them up.
Of course, I'm here so it HAS to rain. Unreal.