I pulled the silencer apart. Removed a heap of steel wool that was in there. It wasn't blocking the inner pipe/causing any real obstructions though. Packing didn't seem over tight or soaked in spooge so I put it back together. Haven't tested yet.
On assembly ensured that there was good contact to the frame on engine mounts and on the coil. Also had the coil removed recently to double check resistance. At the same time clipped both ends of the plug cable. Specced up the same, but also haven't tested since.
Currently have the reeds out, so plan was to install reeds again with the replacement intake boot that I had ordered during the build up. Then see if it's mysteriously fixed itself.
Could one of reeds have a crack or be out of spec to cause the flutter?