I have been on Methotrexate & Folic Acid for several months for RA. I have experienced sore throats and mouth sores (mainly on gums around teeth). My Rheumy & myself found that it just wasn't working by itself so he added Remicade infusions. I have had three and have felt much improvement. It has even began to clear up my psoarisis of which I've had for the passed 2 years!
Something that you have to consider is that with any drug comes side effects and ask yourself, "Will the benefits of treatment out-weigh the possible pitfalls?"

Hope this helps and I hope your daughter feels better soon. God Bless!