For some reason Rootsweb is not sending me notifications to my email when someone responds to my messages, which is the reason for this late response. I just happened to come here looking for more answers and saw your note.
I did receive a response to an email inquiry I had sent to the Yukon Archives in May of 2012, which had some of the answers I was seeking. They gave me some data they found in "a ledger of royalties collected on Bonanza Creek and Eldorado Creek and their gulches and tributaries from 1900 to 1901". I got this information from Glenn Iceton at the Yukon Archives, so maybe you met him when you were there? His email at the time was
glenn.iceton@gov.yk.caI did not find a reference to the ledger in the online finding aids of the Yukon archives.
Because my family came out of the Yukon in 1901, I did not ask for any records past then, so I am unaware of what exists for the later years you are seeking. Maybe Glenn could help you. I know this isn't much help, but it is all I know. Good Luck.