Thanks all. Here's what I have decided initially. Replace shorts with ones with no stitching - already on order.
Put stock saddle back on bike for a while. It is firmer. Until I decide on size and brand.

I have realized I tend to scoot forward on my seat causing pressure on my soft parts instead of sitting on my sit bones. I am going to combat this by getting a shorter and angled stem for my handlebars. I have thought about trying this before. I suppose maybe I could have gotten a smaller bike, but what did I know at the time?... I am 5' 4 1/2" and am on a 51cm bike. I figured that was small enough. So I will try the stem change. I think this will get me into the right position for sitting back on my saddle correctly. I already have the saddle all the way forward. I guess I am shorter than I thought

So tomorrow I will stop at the bike shop to see if I can get a shorter stem. If not then I'll order this one Bontrager: Race Lite 4-Bolt 40 Degree (Model #11233) 40 degree stem.