I really like that program. So simple and so easy to integrate.
Doing the met con workout to "rest" you legs might be a good idea as you're building up your running volume but if running is your weakness then you should focus on running. In the begining you might want to substitute metcons for running but try to phase them out as you adapt to increase of running workouts.
I think one day of full body strength for maintainance combined with the running progam should get you where you want to go. I prefer the strength option to the metcon because it will give your energy systems a chance to relax while working on your goals of improving your running while maintaining strength.
Dont worry about losing to much strength. If you loose a bit of muscle mass your relative strength should go up anyway.