Shorts could help. So could a new saddle.
I'd recommend first taking some time off the bike to let the body parts heal. If they're raw, no piece of equipment, no matter how good, is going to feel good. And when you do get back on the bike, start out slowly....15 miles and see how it goes. Like in the beginning of the season, you have to "build up the callouses" - so to speak - before you're comfortable doing a 30+ mile ride.
Good luck.