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Absorption Problems

Hello All - I am still undiagnosed, BUT now after purposely inflamming my system for scopes (per doctor) I used slippery elm and marshmallow root to calm things down. my body went from optimal thyroid (Im Hypothyroid) to out of range low in the two months between inflamming my system and using the herbs to calm my system
Has anyone else struggled with absorption issues? My doctor put me on a 9 day dose of Prednisone to see if that will help balance my gut out. Im struggling with severe constipation (taking 2000 mg mag citrate capsules) have not changed eating habits for the last year. I am not the typical Crohns patient I guess....... It seems like a constant moving target.
Ive avoided Prednasone for some time due to the reactions I have to medications but nothing seems to be absorbing into my gut at this point!?
Anyone else struggle with this?