I'm sorry you're dealing with breastfeeding issues on top of everything else!
I pumped for 9 weeks before getting my firstborn to breastfeed (then didn't wean him until he was 2 1/2 and I was pregnant with my second) so I hope that gives you some hope that it's possible. I didn't have flat nipples though... But no matter what happens, you've done fabulous pumping this long already and getting him as much breastmilk as you can!
I'm glad you've got LCs to consult, maybe now that Luke's health issues are resolving you'll have more luck with their ideas. Good online resources I've seen are
http://www.breastfeedinginc.ca/products ... ng=English - Dr. Jack Newman, an early proponent of breastfeeding and has even devised ways for mothers to lactate and breastfeed their adopted babies. One note - he's from Canada and prescribes a drug for lactation that is illegal in the US so we can't recommend it here. Instead, I've also heard about Reglan being prescribed in the US for lactation and re-lactating, and a lot of my friends have had amazing increases with supply when taking Fenugreek - though everyone says it makes their skin smell like maple syrup for a while.
Maybe try lots of skin-to-skin time? Even if he doesn't want to actively nurse? My firstborn wasn't happy with the transition from bottle to breast at first, but he decided it tasted better coming straight from me so I got lucky. He never would take a bottle again, though, so I ended up having the opposite problem when I left him with a babysitter.
Good luck with whatever you try and whatever you decide - even if you decide to switch entirely to formula that is perfectly okay!