I got thrush in my milk ducts due to cracked nipples. I needed to take an oral thrush tablet to clear that in the end (was a ilfesaver on the breastfeeding front as it was starting to be agony).

Have you been to see a lactation specialist? My sister went to one and found them really great. Normally feeding is around 10-15 minutes a side, so taking longer than that sounds like there is an issue with something, plus it's obviously hard wear on your nipples. With my son we found he had silent reflux (non-vomiting, swallowing anything that came up secretly), and found that made him comfort suck for aaaagggeees as a way of soothing his throat. I also think that sometimes babies can get used to bottles (they can be less work to get milk from), so might need to stop using them once you're fully healed so she's prepared to put the work in. A specialist though can observe and see if she's putting in a decent effort or just enjoying the suckle and give you advice on this though. My experience with any changes to routines is that there is 2-3 days of complaints from bubs, and then things settle down. 

Seriously recommend getting a family member to pick you up the thrush pill - you can get it over the counter at any pharmacy. It's not prescribed when you're breastfeeding, so doctors just give the gel which does nothing if the thrush has gone into the milk ducts. They actually give the pill to babies born with AIDS, as they are born riddled with thrush (even in their brains), and the pill is the only way to fix it (so it's pretty safe). I used to find the first let down excrutiating with thrush, and it would slowly ease into more manageable pain. Tried gel for a week and it did nothing, had the tablet and noticed a difference the next day, with huge improvement over the next week. Will treat your daughter too via the breast milk, as she'll have oral thrush if you have it (you pass it back and forth if you're not careful), which can give some sore white blisters in the mouth that could effect her feeding too.

I liked the natural papaya gel for cracked nipples too, plus letting them 'air dry' after feeds for a bit (rather than putting the breast pads straight on) to help make a less moist environment for thrush/other nasties.

From memory I think it took me around 6 weeks to be confident with knowing I was doing it all ok, and by 8 weeks we were working together like pros. It is hard work, but if you can get it to be a nice relaxing time together then it's well worth the effort - many, many months of snuggle feeding time to look forward to after all the first unpleasantness is past.