Mary Grace,
I can totally relate to what you're saying - you want something in there so that they'll cut her some slack on her bad days, but not underestimate her on her good days, right?
The same thing happens with my daughter Cassie - different symptoms, but she definately has days where she's right on, and days where just getting up and eating breakfast is a challenge!! My s are going into 5th grade next year, and we're also working on her IEP.
This is the statement we had put in there, in the beginning, where they're describing her strengths and areas that we're working to improve - before the specific goals and objective pages:
"Cassie's academic performance will continue to be variable during her neurological recovery period. Thus, expectations for her must be adjusted based on her fatigue or cognitive status at any given time."
I hope that helps. And, as far as how they feel, the only consistent symptoms my daughters have ever described since their surgeries are headaches and fatigue - and not every day, mind you, but they've never described feeling any thing else related to the MM.
Good luck with the IEP, I know how stressful it can be - but think how relieved you'll be when it's done and you have the whole summer ahead of you!!

Take Care,

Kristen