Hi Lucy, well done for persevering with bf! It's sooo hard to get established, but so easy and rewarding once you get going. I haven't had thrush, but have had mastitis with both of my two (ds & dd) around the 2 wk mark, so sort of know the pain you've had to go through.
Something that hasn't been mentioned yet, could your dd possibly have a tongue-tie? My ds did (has), and being my first baby I didn't realise there was a problem, except that he was finding it do difficult to feed properly, was fidgety, made clicking sounds, and squashed my nipple. Finally the HV mentioned that he could be tongue-tied (4 wks in!!). It was only after lots of research myself that I realised this definitely was the problem. Here are a couple of links to see if you can relate to any of this.
\link{http://www.betterhealth.vic.gov.au/bhcv2/bhcarticles.nsf/pages/Tongue-tie?open\Link 1}
\link{http://breastfeed.com/resources/articles/tonguetied.htm\Here is a good picture of a tonguetie}
I managed to bf ds for 10mo so it wasn't a problem in the end. He finally got the hang of things in week 5-6.
Thankfully dd (4mo) doesn't have a tt, but still makes the odd clicking sound on my right breast, which funnily enough has a slightly smaller nipple than my left so perhaps she finds it different to latch on to when I swap sides.
Also, to help with pain (not sure if it's compatible with your thrush creams) is LANSINOH. It's about £10 from Boots, but is the best cream ever!! It soothed my cracked nipples no end. I had tried lots of cheaper products but nothing worked as well as Lansinoh.
One last thing that comes to mind. My HV said to look at your breast, the shape of it (pertness) and where the nipple is. Now imagine a straw coming out from the centre of your breast and out of you nipple. That is the angle the baby should be held to latch on to you breast. So if your breast is [ahem] pert then maybe you need to sit up straighter and more forward so that you go in at the correct angle. She said if the angle is wrong it will be like drinking out of a bent straw and nothing will come out, or not easily. Made sense to me and did the job. I always think of this if I feel the latch wasn't quite right, I just take dd off, readjust myself and try again. I find that lots of women starting off on bf don't realise how important sitting upright is and having plenty of support under your arms and back. Maybe change bf chairs? Also get a "V" pillow to rest dd on?
HTH and you start feeling better soon.