Jeremy,
I have found it necessary to ignore the plate frequencies or the Helmholtz one, if they are different. On the guitar(s) I mention (the one that's still here) the box thuds at a G, which is the low note that was too loud. And the G string, too. But when I finished shaping the 2nd back brace as described in the earlier post here, the G problem went away, the low E itself became as loud as the new, mellower and quieter G, but the box thump remained at G. Reshaping the 2nd brace is lots easier than anything else! Give it a try.
Just to check, try playing the low E and feeling the back just below #2. If it vibrates a lot, but then that area goes dead when low D is played, it will confirm this as the likely culprit.
Scott
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