Okay, this might be pointless to post but, my wife's Prelude would pulse like you mentioned and it had me going crazy trying to find what was causing it. After quite a while (more time than I'd like to admit here) it turned out that it was a collapsed upper radiator hose. When the engine was warm the heat would have enough pressure to keep the hose "open". When the engine would cool down, the hose would partially collapse and cause the pulsing when it was cool. In fact, I think it also had caused, or coincided with, an air bubble in the coolant system.
I guess I would just recommend taking a look at your hoses and maybe check for trapped air in the coolant system?