It sounds as if you may have jumped in at the deep end with the commuting and are suffering accordingly.

It may be too late now, but for most people going back to cycling after a long break it is usually advisable to start off with short cycle trips, say 20 - 30 minute duration, certainly not so long as brings on any discomfort. Get out for as many short journies as you feel comfortable with and you will gradually find you can cycle for longer periods without pain.
Only after finding yourself able to cycle say twice your commute distance would I consider actually cycling the commute.on a regular basis.
Bending the elbows and transferring more weight to your feet to ease weight on the seat when going over bumps helps to ease the shocks to your body and make the ride more comfortable.