Oh yeah.. I know about new pains when starting to use muscles that have been dormant for a while. One thing that works for me is a foam roller, but you can improvise with many things. Here is a video that shows a pretty good foam roller routine. Monkey - meet football - LOL http://www.youtube.com/user/ecressey#p/u/89/8caF1Keg2XU
And for running barefoot - I say go for it. Find a grassy park and kick off the flip flops.