While everyone has different reactions to medications, the dosages of Methotrexate used are miniscule compared to those used when it is infused as a chemotherapeutic agent so you're the first person I've heard of having "chemo head" as a result.
MTX is usually used in conjunction with Humira due to certain synergies. If you are suffering I urge you to speak with your parents and/or gastroenterologist to discuss your treatment plan to address this.
I have had Crohn's for 42 yrs now - dx when I was 24 yrs, now 67! I was on mtx tablets 25 mg weekly, then 25 mg injections (done at home weekly), but after having some serious flares and surgery (right hemi-colectomy) 3 yrs ago, I was put on Infliximab infusions, every 8 weeks as a day patient in hospital. This caused enormous weight gain and I have just recently gone back onto mtx 25 mg injections which is working okay. I have other Crohn's complications such as pancreatic insufficiency, for which I take Creon enzymes with each meal, and Colesevelam for bile salts. We cannot prescribe any drugs as a lot of them are toxic, and can only be prescribed by a Gastroenterologist. I would suggest you have a consultation with your own gastro and heed his advice - they are the experts, not us!
Take care,
Liz.