I think Harvard is looking for unique and compassionate applicants not just numbers. If they really like you they will try their best to get to know you and therefore grant you an interview. If you think Harvard is the best for you then just apply.
I also applied to Harvard but kind of late. Like 3 weeks ago. All I have recieved is a letter saying that they have my application, and a timeline of events. I don't have the timeline in front of me, but I don't think its too late...
2) apply now and at the worst lose about $200. i'd say if you're not dead broke and you don't want to regret not at least giving yourself a chance then throw your hat in the ring and see what happens. it seems that harvard takes their time so you could still have a decent shot at it.