The German drafting supply firm Staedtler makes a set of colored, very-fine-tipped markers that work well - if you're trying to cover a dark color with another dark color. A fine Staedtler pen probably would work well for the black spaces between the yellow pilasters. But covering the black plastic with a yellow marker would, I suspect, be hopeless.
For what it's worth, I think that transom looks mighty good. Getting all those pilasters to look identical is close to impossible. I can state with certainty that yours looks far better than any of the ones I built did.
If you feel like touching it up some more that's certainly commendable. But if you can't make it any better than it is now, these 64-year-old but pretty critical eyes won't mind.
One thing I would take the liberty to suggest: consider doing something about those oversized round bosses that the stern lanterns fit into. They're conspicuously out of scale. Once the lanterns are in place, the bosses will be less noticeable, though. Again, if you can figure out how to get along without them the model will be improved - but it's going to look mighty nice in any case.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.