Sounds like you found the problem! I would remove the header and place a small dent in the tube where it's rubbing. You might be able to dent it without removing the header but it will be difficult to place a dent in it without removing it. On a set of E-Body Hookers I bought used,, the drivers side tube had a large dent in it,,(The number 7 cylinder,, the last one on the drivers side),probably from the same symptoms you described!
I sold them after my engine dyno testing. I'm gonna use either Dougs or TTI's, both very expensive but fit very well! Good Luck,,and let us know how it turns out.