There are numerous threads on APC concerning color deficiencies. You should search them and familiarize yourself with the *real* process. What you need to do for a FAA exam is different than what you needed to do for the Navy Flight Physical.
As far as the school....I also suggest that you search for threads with the school's name in the title. You will find abundant information.
If you want one side of the story - search for posts from SkyHigh or PM him when you get enough posts and he will certainly enlighten you to the future hardships that you are setting yourself up for in the future.
GOOD LUCK!
USMCFLYR