I replaced my alternator with a 135 amp alt about a month ago (running about 3000 watts in my system) but my old one was about to go before I replaced it. It was pulsing like you say, thats a classic sign of failure. Mine would come and go, but eventually the alt will fail. Before gettin a check up, or replacing the alt (fairly easy) check battery terminals to make sure you have a good connection... it is possible you have an engine problem unrelated to the light pulsing, but more then likely its your alt. Also consider getting a decent aftermarket alt.... not much more, plus handles much higher loads and lasts longer... mine is an alterstart (got it on ebay).