I can see the dilemma here... It sounds like the prednisone was suppressing some inflammation around the body, possibly inflammation caused by the fungal infection. THe problem is, that Prednisone has some immuno-suppressive actions as well as anti-inflammatory actions, and can really slow down the healing process during recovery from a fungal infection. Therefore, to gi veyour kitty the best shot at killing the infection, the prednisone must be stopped.
Now, there are still other options for inflammation and pain, without suppressing the immune system, so all is not lost...
Buprenorphine is a nice painkiller for cats, it is related to morphine and can be applied to the gums or under the tongue 2 to 4 times a day for pain relief. Metacam is an anti-inflammatory that has to be used very cautiously in cats, but can be used if there is significant inflammation going on.
I hope this was helptful to you -- let me know if you need more info.
Good Luck,
Drew
If this answer was helpful, Please click "Accept" so that your deposit can be paid to me, in return for my time spent helping you and your pet.