I have to agree w/ David that a good sign painter is your best bet. Now finding one is another story... Right before I stopped restorations, I found the best sign painter... Wish I had found him ten years earlier!
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As far as the vinyl decals are concerned, they'll definately be cheaper but I'm not sure how they'll look on the embossed lettering...
To answer your original question...
If my memory serves me, manufacturers had special rollers to paint just the top of the embossed lettering.