I am also taking summer school, but I added those classes as planned because I have already signed up for them. However, I plan on sending in my app june 1 just so everything can be verified, and then updating my transcripts once my summer grades have been calculated. The schools won't hold your app. I suggest just applying to one school just so your app can be verified, then once you have raised your gpa with the summer classes, applying to all the schools you want to.