Good job! Yes it is necessary to manually remove what you can, then let nature take over. I hope the berghia work for you. When you get them don't forget to turn all the pumps off until they settle in your rocks. You may also want to wrap your wave pumps with a screen of some sort to prevent them from getting sucked in, if they ever get that high.Update.
I ended up removing pounds and pounds of bubble algae and xenia. I was originally going to go after the Ap. initially, but just found out most the Ap. was connected to the BA. So I went after the xenia, BA, and Ap. After the removal I used F aiptasia to kill as many as I could find. I did a water change at the end of the removal process. I didn’t take any rocks out to try and deep clean but may need to do that soon. Took me all day but was worth the hard work.
My berghia are in coming today so I hope they are healthy and ready to eat.
(Some progress photos too.)