First off, definitely consider losing the running as punishment thing. I do it so seldom that I can tell you about each time I've done it in the last five years. It is easy because it was just once and the girls were so surprised and shocked by it that they were actually apologizing to me after it was over. It simply doesn't work with girls and they will be bothered by it.
You can coach boys and girls the same. However, never forget that they are not the same.
I've coached girls for over 12 years and the best advice I can give is that you must really watch what you say to girls. Boys hear exactly what you say and nothing more. Girls hear completely different things, often something that really isn''t even close to what you've said. For example, have you ever said to your wife after running into a friend you haven't seen awhile, something to the effect of, "Gee, honey. It looks like Jill has lost some weight" only to have your wife hear, "Gee, honey. You're fat!" ???? I know you have!
That is what you deal with when girls are around. You have to anticipate what the girls might hear whenever you attempt to correct them or impart discipline. You also have to be careful about overly praising a girl in front of the whole team (praise several, it will work better) because if you do, one or more girls won't hear the praise, they'll hear, "He said I suck."
You also can call girls out for mistakes, but it helps tremendously if you explain that you are not picking on them but you saw this as an opportunity to teach something to the whole team about what not to do and what you'd like them to do next time it comes up. You then can thank her for bringing up this splendid teaching moment and tell her she's awesome and that you know she'll get it right because now she knows what to do and all will be fine.
Oh ... and about the criticism. Remember, they are girls (who will be women), and that by nature they are more self-conscious than boys (or men) and that again, by nature, they will spend more time than males do analyzing and trying to fix things that aren't quite right. Because of this, they will respond much better to coaches (men, especially) who spend more time appreciating the things they do right rather than those who feed their already overworked self-consciousness.
Absolutely awesome post. Thank you so much for the responce. I have definitely already decide to remove thne running for punishment as I believe I can accomplish what I want in a more effective manner.