You can use Stew Mac's Black Fingerboard Stain to give it an ebony look. I've never tried to stain one with the frets already installed though, but I imagine it wouldn't hurt anything. The only concern is with the inlays, try not too stain them directly somehow if your not going to pull the frets. You could try it first and if it doesn't give you the results your looking for, you will then need to remove the frets and do it that way. If your not really familar with fretwork, then I'd consider avoiding doing this, since you'll want the fretjob to be accurate as can be. You can pull the frets by heating them up with a soldering iron, and slowly prying them up starting at one end and going across the length of the fret. Installing new ones could fill up a whole article on it's own, if you want to do the job right. Please only mess with the fretjob as a last resort.
As far as getting the old finish off the fingerboard, you can use Naphtha (lighter fluide) to remove it. That should work unless for some reason it has been clear coated, which would suprise me since it's usually only done that way on maple fingerboards.