Looking at the setup, I'd say you need to start dialing in the fit to improve your comfort. Really, this is just moving the saddle and bars small amounts to get the right position on the bike.
You could start with this fit calculator to get you in the right ballpark.
I expect that bike will handle 28mm tires, which do help on the chipseal. I have some of these that ride pretty nice and last a fairly long time.