Compositing a second instance of a movie clip onto itself

I have a tracked video in which a building extension is added (please, everybody, this is still a WIP). In front of the extension are trees that I have masked out of the front of the building. Yet there are still branches that need to be masked and added on top of the building. The problem is that in the original clip, these second branches fall in front of a window in the original clip so it’s not a simple case of masking/matte. My solution would be to composite on top other branches from the movie clip and tracked via a marker. Yet I can’t seem to get this to work correctly. I’ve tried to parent the second instance of the clip and its mask to a pertinent track marker but being how the second instance is Translated into position it follows the track at the translated location/rotation, veering Northeast. I also thought maybe doing a 2D track on the movie clip and compositing that on top but apparently you can’t do a second separate motion track in the same project.

I hope I was clear on what I’m trying to achieve. Maybe I’m overthinking this; I’m sure there’s a simple solution but it’s escaping me. Any help would be greatly appreciated. Attached are two images that hopefully clarify a little more.

BONUS UNRELATED QUESTION: Can you render a 2D Stabilation track locked to selection?
– GT

Trees are the bane of the compositor, with their complex complex outlines and the fact they move…

Could you create a png of the branches that you’re having a problem with… and bring it into the 3D scene?

I tried your suggestion. I took a frame from the video, did some processing in Gimp, then placed it in the 3D scene using Image as Plane. After some positioning, scaling and a Copy Rotation constraint from the Camera, your method does indeed work. Thank you.
I imagine with some object masking directly in the 3d scene this method would also work with a movie clip/image sequence.
Thanks again!