Yeah, your options:
1) remove the fretboard, replace it with a new one with dots, refinish (not cheap)
2) you could have the birds removed somehow, put in dots and fill the rest of the bird routs with some sort of filler, then remove all the frets so you can sand it all flat and then put new frets on (not cheap and also would look terrible).
3) have some custom stickers manufactured that look like dots and rosewood that you stick on over the birds and then replace every so often as they fall off / wear out.