Hi Rachel,
Much good advice has already been given by the wonderful BP community.
In addition to all of the positive ancillary factors about the property (location, transportation, crime, etc.) trying to educate the seller is a main goal of most realtors. And, unfortunately some home owners just think their property should be sold at "x" price, which in most cases is higher than anyone wants to offer.
And, although she has lowered her price from $540k to $500k, there may still be a huge difference in the actual value and selling price and unless the seller is motivated to sell, that price may remain high.
I agree that the upper floors (attic) may provide an additional 2-3 bedrooms, that might not actually be legal. My SF home eerily sounds the same, as I have a 6 bedroom, with 2 BRs on third floor, but our 2.5 bathrooms easily accommodates our family of six. Thankfully, the family before me that raised six children legally added the upper bedrooms.
Back to you, once you perform additional due diligence, and determine the ARV, if you still like this house, and the numbers work, you can still offer some number that you are comfortable, say, $300k cash. The seller can only say "no." Of course, make sure the numbers work for you.
Good luck.