An alternative possibility
This is a speculative alternative hypothesis to what might have happened here.
It is possible that the original builder mis-located the F-611A+B bulkhead, and the associated stabilizer attachment bars, by 1" too far forward, but everything else about the build was correct. Remember the -6 wasn't pre-punched, so a builder measurement error is possible. And any carpenter will tell you how easy and common it is to have exactly 1" error. The F-611 bulkheads would have been too narrow to fit in the mis-measured location, so a skin doubler could have been added, or the flanges on the bulkhead adjusted so that the bulkhead fit.
The builder would have discovered this error when it was time to mount the horizontal tail and fin. The 1" shim blocks would then have been added to correctly position the horizontal tail and everything else would have fit correctly.
So now, along comes an IA and says this isn't right, takes the shims out, moves the horizontal tail forward 1", and we don't know what he did to make the fin install.
Yes this is speculation, but it explains some things, like why did the fin fit correctly before, as evidenced by the photos.
Ultimately, someone with good knowledge of RV construction, and a set of plans, needs to look at this airplane.
And none of this readily explains the OP's original question about the rudder flutter. That is very likely misaligned hinge bearings and/or not tight jam nuts on the hinge bearings.