Re: theme & header navigation
I think it may be easier for you to create a Child theme based on the bp-default theme, that way any files that you have not directly coded will still be in use.
For more info you can read this: https://codex.buddypress.org/how-to-guides/building-a-buddypress-child-theme/
What I did was took the default theme style.css and began to modify it by loading it in a child theme (leave the bp-default where it is, in your child themes css template header call Template:bp-default). Then the need for a custom homepage arose, so I just created one. I did all this and all of the buddypress functionality stayed in place because it was loading from the bp-default – without ever having to re-code every single .php file.
For you, since you have an existing theme, I would load your stylesheet as a child theme, then modify it to match the bp-default architecture(i.e. #content becomes #container, etc). Then you shouldn’t have to rework every single php page, because your style will load using the buddypress theme structure!