You could mess around with the seatposts a bit if you wish. There are some suspension seat posts, generally used on MTBs. But, there are some more modern road seatposts that also have a little flex. Look at the Specialized Roubaix.
Different seats?
Padded handlebars, or perhasp gel pads for handlebars.
I see you can also purchase Shock Stems.
To me, that would likely be mighty annoying, but I suppose it couldn't hurt to try, perhaps I'd be surprised.
Personally, I like flat topped "aero" handlebars. They are much more comfortable than riding round bars from the tops.
"Ride Light". Avoid big stuff to run over, and stand up when you see something bumpy ahead.