First off, unless you have some constraint like you plan on not applying to ANY schools if you get a certain score, I would complete and submit your app now with the MCAT pending.
If you have above 3.0 GPAs, there's no reason for you not to submit your app now, in fact it will hurt you, because if you don't submit until mid-Sept, it will take you 5+ weeks to get verified. If you are applying regardless, pick 1 school and submit your app to them now. Then after your MCAT score comes in, submit to the remaining schools. This is in your best interest.
As far as submitting your transcripts go, you can submit them absolutely any time, as long as you have an AACOMAS ID number, which you have if you started the app. The only reason to delay sending in a transcript would be if you have classes whose grades haven't come out yet, and even then its only if you want to save the money associated with sending another set of transcripts later.