When I went through, the MECEP'ers had a higher standard than the normal MIDS on getting a flight contract. There was a MECEP'er who had better grades on the tests than I did, and he didn't get the contract while I did, so FWIW. No idea on if there were other circumstances, he ended up with a NFO contract.
Timeline wise, I didn't put in for my contract until early to mid way through my senior year and heard back a couple of weeks prior to commissioning, mainly due to waivers that I had get for Cardio, and Ortho stuff, and that took an extra month or two to get that stuff in. So, while you should start early, you don't have to worry too much if you don't get it in early.