Check the exciter wire thats on the top of the alternator, there known for being damaged/broken and causing the lights to pulse. My alternator took a crap about 2 months ago and my new one still has the lights pulsing issue, but atleast it's not causing my trip odometer to reset like the old one was . But yea, check the little wire on the top of the alt 1st, LS1tech.com is a good place to get some info about your problem also.
Chad