I love the idea of a program schedule that incorporates running or any other type of cardio. I run about 15 miles a week while doing DB Kettlebells - sometimes I layer a run with a full workout from the program and sometimes I skip the program workout if I had an esp. hard or long run. I love the recovery workouts - I think they've really helped with my running program.
TBT was good for shaping my legs. Lots of lunges and squats :)
I haven't done the BHT workout, but I've found that when I am intensely sore after a workout like that, working the same muscles again the next day can actually alleviate some of the tenderness. It gets the blood flowing to those areas and gives you another opportunity to stretch during the cool down.
I've been going for short (3-4 miles), easy runs on one of my two recovery days from TBT and have felt fine. I think it's all about listening to your body and making sure you're taking in good nutrition to help your body heal.