Even with better footage, this proved to be quite a time consuming process. I had to come up a custom workflow:
- Cut chosen footage into chunks (because for each scene, we did several takes and left the camera running)
- With each chunk, number them so that they could be played in order
- Import a chunk, one at a time, into After Effects for chroma-keying
- Export the chunk with the alpha channel intact ready for editing in Premiere

Some footage required manual intervention using masks to clean up unweildy marks.

I combined the techniques of both of these tutorials: