While I still believe in applying early, one reason being that you can just get the preliminaries done with, I can definitely see Emergency’s point. It definitely won’t hurt to start the process early…getting together any transcripts from schools that you are not currently attending, putting together your PS, working to make sure that your letter writers have forwarded your LORs to interfolio, or any other service you are using. This way when you decide to submit your application, you won’t have as much to complete it.
I would say apply in the beginning of the summer and report the second O-chem as “in progress”. You can update the schools later with your fabulous grade. Getting through the AMCAS verification process and getting those secondary, school-specific applications in your hands to work on can be time-consuming tasks and you don’t want them happening in August. I’ll be September by the time you’re really complete and many of the early interview dates will have been given away by then.