I'm still pushing forward on FTA, thought I'd post for other people running into issues.
Tried entering my classes again. It's accepting them if I put the actual dates of the rotations instead of trying to group them by semester. A few snags related to communication between the military and my school, but I've been told that after I get one last issue taken care of my application looks good to go.
Still worried I'll get denied over the 45 hour credit limit but we'll see...