my only suggestion is using my notch filter. Is the instability frequency above 4 hz? Sorry I can't remember. If so, you can cherry-pick my notch filter into your PID library.
clone my repository onto your machine
get into the directory for my repository on your computer
then checkout my 3.4 branch. type "git checkout Copter-3.4"
now add my ardupilot repository as a remote to your current repository
get into your the directory of your repository
type "git remote add ardupilot "
Fetch my changes
type "git fetch ardupilot"
cherry pick the commit that adds the notch
type "git cherry-pick 34c5dda"
lastly you can remove my repository
type "git remote rm ardupilot"
at this point the changes have been committed to your local repository. You can then push them to github when you are ready. there should not be anything that you changed in developing the dual configuration that would affect my notch merging cleanly with your repository