Padded bike shorts? Is it possible your chamois is too thick?
And exactly what part of your lower extremities? If around the sit bones, perhaps you are sitting too upright. If between your number 1 and number two, otherwise known as the perineal nerve, then I can only say keep trying saddles. For me, less padding in saddle and shorts gives me better results. Moving the saddle a few mm fore or aft has made a big differences too.