My general rule for bike shorts is, that they should cost at least as much as the number of miles you will be riding in one ride. For example, if you are going to ride 50 miles, you should spend at least $50. Century ride.....$100

Now that comment is a little in jest and doesn't really address the other issues about which you have gotten great advice, but thought it did answer your original question.

Sounds like a saddle fit issue to me, but let us know what you find that works.