It sounds to me like some of your symptoms are from flaring and some "could be" MTX related. When I first started MTx the main symptom I noticed was extreme fatigue. Just when it would start getiing better it would be time to take it again. I have been taking it for almost 2 years now (10mg a week) and I hardly feel any side effects.
I have noticed that sometimes I have more mouth sores from it. I think your body gets used to the meds.
Sometimes you may be more susceptible to other viruses that are floating around, too.
All in all, if the symptoms bother you too much or you are not sure what is going on the best thing to do is call your doctor and let him know. I am not in the medical field, just sharing my own experiences with MTX.
I hope that you will be able to feel better soon.