Sorry to hear you're having problems. Not sure if this is relevant to you, but wanted to post it in case it could help any one else avoid what I went through.
I had a thrush infection following mastitis when DD1 was born (she's now 2.5), which lasted from week 3 to week 16. Nystatin (drops)worked on her, but not on me (cream) - I later concluded I'd actually developed a deep breast infection(not an abscess), which caused my breasts to feel as though they were filled with hot oil - before, during and after feeding. It was absolutely awful, and I so nearly gave up bfeeding. I didn't know any better though, and thought this was normal!
Fortunately I got some fantastic support from both the NCT and La Leche - a counseller watched me to check dd was latching on ok (my GP thought this might be gthe problem). She also gave me some US literature about deep breast pain, which suggested that the most effective treatment needed to be tablets (ie internal). My GP disagreed, as he said he couldn't see how anti thrush medication could reach the breasts via being ingested - his view was that it needed to be a surface treatment (except that my infection didn't feel 'surface' by this point).
In the end, I happened to have an appointment with a locum one weekend, when I was tearing my hair out. I asked why I couldn't be prescribed the treatment recommended in the articles. His concern, which I did understand, was that whilst studies had been done on their efficacy with women, and with infants seperately, none had been done on breastfeeding mothers. However, he checked the likely levels that my dd was likely to get via my breast milk, and decided to allow me to have the medication.
To my amazement, what I got given by the pharmacy was Diflucan (ie the one tablet cure for vaginal thrush). After 13 weeks of agony, the pain disappeared in 2 days.
I'm not saying that this works in every situation, but it certainly worked for me, and meant that I started to enjoy bfeeding for the first time in 4 months. I was able to continue for another 6 months after that, a fact of which I'm really proud.
The sad thing is that it's no wonder there are no studies on this type of treatment. My GP admitted that most women in a similar situation will give up bfeeding, and hence won't necessarily present themselves at the doctors with symptoms. To give him credit, he and the other GPs at the surgery decided to review their handling and advice given to this type of case, after my symptoms cleared up so promptly. He admitted that he'd just not encountered a case of deep breast pain before, that wasn't an abscess.
I do hope you manage to cope with the discomfort and start to enjoy feeding. Please let me know if you want details of the studies I was referred to - there are a couple of helpful websites which may help.