I will start with history since I think it's relevant in this situation. Thank you in advance for taking the time to read this, I know it's a bit long... my apologies.
While searching through an online adoption site we found a cat whose owner had died unexpectedly and the owners best friend was trying to find homes for all of the owners animals.
We filled out pre-adoption paper work, submitted it, received information on the cat regarding her life, personality, health etc. and agreed to meet foster parent. The ad was listed incorrectly and we found out that she actually was out of state so we agreed to drive over 3 hours and meet the foster parent half way. The cat was sedated (which I can understand having owned a cat before that didn't travel well). It was dark by the time we arrived at the meeting place (the parking lot of an outlet mall). Having met in a parking lot we didn't get a chance to really spend time with her and since she was sedated it was hard to tell much about her. Not the ideal situation to say the least! The cat had just been vaccinated, and been professionally groomed and had a sanitary clipping. Our adoption fee was very reasonable ($60) and covered what had been paid for vaccinations/grooming for which we received receipts/paperwork. We stayed in a hotel that night and when we settled in and took the cat out of her crate we noticed that she was covered in sores. It was obvious that she suffered from severe itching and could barely stand to be petted without incessant licking. She is tremendously shy and took over a month to acclimate and actually come out of hiding (aside from eating/litter box) so I thought her sores might be from stress of being moved around from home/home... now multiple times. I gave it a few months and saw no improvement but didn't want to make things worse by bathing etc. I finally decided to start her on monthly flea/parasite treatments since I treated my dogs as well. After a few weeks the sores finally went away although she still has trigger points that when you pet her there she begins licking and its obvious those places itch. The sores remain at bay as long as I am VERY consistent with the drops but if I am late even a week the sores reappear. They begin UNDER the skin and then surface scabbing over and spread rapidly. I haven't let her go long enough for the sores to spread as badly as when we got her because to me it's just cruel but I suspect they would take over her entire body. Since she is a long haired cat she requires regular grooming but because of her past she isn't keen on it and it is difficult. I have managed to comb her with a flea comb and to date have yet to find a flea or even evidence of fleas (eggs, excrement etc.) We have been battling ear mites, she is VERY hard to treat, having her history and I suspect wasn't cared for like she should have been and has no exposure to that type of handling. So... my question is... what could this be?
Thank you for your time.

I've had cats all my life, but am not a vet, so I cannot give you a diagnosis (since I can't examine the animal, plus I don't have the credentials). Have you taken her to a vet? Seems like that's the place where I would start investigating this.

What are you using as flea prevention?

I second the thought of taking her to the vet.