It might be worth considering changing the saddle if you haven't already done so? My first bike had a womens "comfort" saddle which may have been the biggest fib ever told. I changed it for a rather more streamlined saddle and it has felt like a different bike ever since.

As regards shorts, I mainly ride for transport at the moment and use padded liners under regular clothes. I like padding at the front, and also a bit at the sides but don't like bulk. I rate my Sheila Moon liner and my Gore shorty, and I have a winter weight pair of Terry tights with a nice chamois too. All without anything else underneath them. Arnica tablets are very good for any post-ride discomfort.