Interesting approach to fret markers.
If dye you must,
Fiebings is pretty much the repair and refurbishing standard. One bottle is a lifetime supply for the average player. Caveat: This product will stain virtually everything it contacts. That includes concrete, fabrics, and skin. Wear gloves.
As far as the dot markers go, the easiest way to remove them is to use a center punch. Punch in the center and pick out the pieces. If you plan on dyeing the neck, do it first. Then color filler to match. Finish by touching up the neck and oiling.
Oil will darken rosewood to deep browns and/or purples depending on the species and individual characteristics of the fingerboard. Plugs can be cut from scrap rosewood to fill the dot holes. Done carefully, the repair will be almost invisible.
Rosewood is great looking lumber. Clean it. Oil it. Learn to love it.