We are in the same position (we won EI at Bedford, but did not qualify to compete at MSC.)
From the Guidelines emailed to EI teams:
"All recipients of a district Engineering Inspiration Award are invited to interview for the Engineering Inspiration Award at the 2014 Michigan FRC State Championship. This interview is conductive irrespective of your team qualifying to compete at the event. Additionally, winning the Engineering Inspiration Award at a district event does not qualify your team to compete at the state championship."
I consider the last sentence to mean that you will not be competing for any other awards.
Good luck to you guys! We are in the same situation as you of winning in the last week and being over a month behind in preparing compared to our competitors. It is an excellent exercise for the students, though.
