Would a Fine tipped permanent marker work?
Find something the color you want (doesn't matter what, ink, crayon, whatever) and fill the number with it, but not all the way up to the edge. Then fill the remainer of the slot/groove with clear fingernail polish. This dries to a semi-hard consistency that can take a bit of a beating before it wears and can be touched up without a lot of hassle. Dries to usablility in less than an hour. Or you can try clearcoat varnish or some other very hard clear coat material for paints, stains, etc. They all work to one degree or another. If you really want to get radical (and risk unbalancing the dice) you can use a very fine tipped wood-burning tool or something similar to scorch the numbers in. I've seen them all used with various degrees of success. The key to remember is, if the color is not OEM, it will probably need frequent touchup. *sigh*
Although this thread is quite old and I am sure the OP has long since resolved his problem, I just went through the exercise of inking some new dice that went really well.
Here is how I did it:
1. Clean the dice with soap and water, rinse, and dry off.
...I used an old toothbrush and dish soap.
...I actually used rubbing alcohol after the rinse and dry, but this probably wasn't necessary. It is also possible that the alcohol could cause the plastic to swell if the dice are left submerged for long enough.
2. Put on some clean, dry gloves to keep the dice clean.
...I used disposable latex gloves.
3. Carefully ink the numbers with a fine tip permanent marker.
...I used a Sakura micron black 02-.30mm tip.
...I was able to wipe off stray marks with a paper towel and re-ink indivual faces as necessary. This didn't happen often since the number grooves will guide the pen tip.
4. Bake in an oven for an hour at 200°F.
...Be moderately careful here, the dice may become soft and you may be able to deform them in handling while they are still hot. You should be safely below the melting point at this temperature (melting point for PMMA is about 320°F)
...I baked the dice on a paper lined baking sheet.
Results:
The marks are very clear and do not come off even with pretty vigorous rubbing with my finger, that includes stray marks. I am using opaque dice so I cannot say if this process would cloud transparent dice, but I don't think it would.
Previously, I tried inking some dice without cleaning them, using gloves, or an oven cycle. I left the dice to dry for 12 hours and the ink came off with handling.