What part was hurting? I can ride 75 miles now without getting sore. After that my neck gets a little cramped but I'm starting ensuring I move my neck around rather than looking straight continuously. When I first started riding, I could go 50 miles before getting sore. I also shift my hands around vs keeping them in the same position on the bars.
I think a big part of comfort is bike fit. Plus I also make sure to stand out of the seat every 15 minutes or so, just for a few seconds.
I'm still working on the whole running thing. I use to be a runner 10+ years ago. I want to get into triathlons. Just joined the gym so I can do some laps also.