if it's designed for another application you would definetly need to plug those holes as they would be after the filter and a direct shot for debris and trash to get into throttle body/engine. you can bypass "valve cover vent" but unecesary if you have the inlet on the intake for it, depending on location of the other fittings that aren't being used you could plug them by running a hose of same diameter from one to the other preferably on bottom of intake and unvisible, other than that they do make rubber caps you could place over top of them, here again dont place anything inside of them in danger of being sucked into engine