Putting her in a bag is going to stress her unecessarily. Is there no where else she can go? If you have a large bowl/vase/plastic container, you can transfer some old tank water, dechlorinated tap water and lots of gravel from the established tank and she should be ok in there (make sure the room she's in stays relatively warm). You also need to consider that a bag doesn't allow you to calculate volumes effectively and also means there is no water circulation - all very bad things when you are trying to treat - especialy a bacterial infection.
You didn't mention any lumps before - this is bacterial and needs antibiotic treatments. I've used interpet's treatment number 8 (anti-fungus & finrot) for columnaris and their anti-internal bacteria treatment is also effective for the sorts of 'lumps' you are describing (if tthe mouth 'fungus' is gone, you may as well treat with the antibiotic now).