The guy at the Church History Library sent me the ledger account from the Perpetual Emigration Fund (PEF) for Eleanor Vaughan.
I am still trying to get an answer for the date, but I believe it is a reconciling of accounts in the 1860s. There are no payments for Eleanor with a debt still owing for $47.03. The PEF managers apparently didn't have any better idea where she was than we do as there is no ward or town indicated. While this doesn't help much, it doesn't contradict our main theory that she may have died shortly after March 1857.
With regard to the debt owning, I guess we can make donations to the modern PEF, the Perpetual Education Fund. That helps poor LDS young adults around the world who need access to educational opportunities. The funds are much better managed today making the recipients responsible to pay it back for others to use. We've made some payments that probably would even clear the interest since Eleanor's debt, but there's no harm in continued contributions!