Stumped and Frustrated with a Holley 670 Hesitation

You'll only know when you drive it with the changes. My only other thought as I read through this for the 1st time is that there may be something hanging up the secondary butterflies; if so, the pump shot would be gone by the time that the delayed secondaries opened and it could bog. Having the throttle hang now might be a symptom of that. And the whoosh you heard upon throttle close could be the secondary hanging open.

I'd disconnect the secondary vacuum pod from the secondary butterflies and check for free secondary action very carefully. Then pull the pod off and check for free, smooth operation of the rod with a vacuum applied and relased. (Sukcing a vaccum by through a piece of vacuum hose will work.) Pretty easy to do.