I don't see any point wasting effort to paint and ballast track that's going to be hidden inside a tunnel. I would lay the track before building the tunnel, and definitely lay track before trying to run trains there...
After you lay the track, and before building the tunnel, I would put a piece of masking tape or something similar (less sticky, so the glue doesn't get on the rails), so you won't get plaster or dirt on the rails. It will be a bear to clean after ward, and simply unzipping a piece of tape is really a lot easier than trying to invent something to clean track.
Make sure you can get to the track somehow. Every piece of track I have made inaccessible has had problems, like derailments or locomotives stopping on it.
When it absolutely, positively, has to get there (someday), ship on the ES&BM.