Catrin, sounds like a gorgeous hike, and 11 miles is a lot no matter how you slice it. I would be hurting too -- though not sure if I'd be cramping, just tired and sore. I hope you can get to the bottom of it. I tend to let all my aches and pains go, since we're on the road and getting to my doctor (or any doctor) can be a non-trivial thing, and more often than not, the problem just goes away with rest, but I know that is not the case for every ailment! 
Has anyone been to Natural Tunnel State Park in western VA? We are here now and did a nice hike today after setting up in our campsite -- around 4.2 miles in the lovely woods, pretty easy, just some climbing and switchbacks, but nothing too rocky or strenuous. We haven't seen the Natural Tunnel yet. That's on tap for tomorrow, our only full day here, plus a few more of the trails here.
Emily
2011 Jamis Dakar XC "Toto" - Selle Italia Ldy Gel Flow
2007 Trek Pilot 5.0 WSD "Gloria" - Selle Italia Diva Gel Flow
2004 Bike Friday Petite Pocket Crusoe - Selle Italia Diva Gel Flow