I completely know how you feel. I went through a similar situation when I adopted Demon from the humane society. He had coccidia that he was never treated for.. and developed a full blown URI 2 days after I adopted him. He ended up having feline herpes and has URI flare ups when he's stressed. Luckily they have been minor and don't require medications. Just the odd sneeze here and there or one eye will run for a day or 2 and then stop. All my cats have now been exposed. I sure wasn't a happy camper at the time. LOL
Sometimes the URI will seems to take forever for the kitty to completely kick depending on their immune system. With Demon it was around 3 months total but he was only medicated 3 times for one week at a time. My vet won't give meds unless it's turned from viral to bacterial. Clear discharge is ok... yellow or green.. more meds.
Definitely contact the humane society and explain that she still has the URI and see if they can get their vet to check her over at their cost since she had it when you adopted her.