:hug: Well, I've had Crohn's for many years, and I have to say the limitations tend to change drastically between remission and flare. My advice would be to list your limitations during a flare as thought that will be your new normal, so to speak; that way if you feel better you can choose to do more but if you are struggling your superiors won't expect too much from you.
There is also the matter of stress, which is a trigger for the disease and also seems to make flares more intense. I'm sorry I don't know what an MEB is so I can't help you there. If you provide a few more details about your assignment/skill set, I may be able to offer more advice.
Personally I was unable to lift heavy objects (I used to lift weights and was very physically fit before I got sick), I needed close access to the restroom, and more frequent breaks. In the private sector this was unacceptable long term and so I ended up on disability.
My father in law and his brother were both Marines, and his brother served when he was first diagnosed. He was taken off his deployment overseas and ended up serving his tour on desk duty. He was an enlisted man, I don't know it that makes a difference in your situation.
I hope this helps. Best wishes on your health and career, and if I can offer any more advice, please feel free to hit me up here or in a PM.