As has been said, there is no substitute for time on the bike and the corollary is there is no substitute for experience. Many issues will be resolved with time.

Saddle fit is a difficult issue. I thought my saddle issues were resolved, after a long and painful beginning. The last club ride, only 37 miles, again was painful on a saddle that has been very comfortable. One thing that has changed is I've lost about 10 pounds in the last 3 months. So 15,000 miles after beginning to cycle, I'm back to working on saddle fit.