I ended up creating a row of airplane windows – making that a composition and inside VC Element, I created a 3d null on the airplane. I copied the position data of the null to the airplane windows comp
If you have a powerful enough machine and most of all a powerful graphics card. I would just do a XML export from FC and import that into PPro and edit in native.
Are you using plureyes to line up audio? I have had problems with that software. If not, maybe you can do a mix down of your audio track, without the filters and then add the filters on the new mixdown track. What I mean is, export a new audio file and then relay that file under your video. I am just guessing as to what I would do.