Rather than touching up the bad spots, look into refinishing the whole thing for a more uniform appearance. Word of warning. Browning finishes are very hard, like the clear coat on a car. Or send it to someone who refinishes stocks.
Check with $rowne!!'s. I think they carry stuff to re-do a stock. If the nicks are deep, don't short yourself ion the sanding. A poorly sanded stock will look bad no matter what coasting you use.