You're sort of in a bind.
The services like fantasyauctioneer require that everyone connects in... you could maybe do it if you had everyone log in, turn off autodraft, drop out, and then have other people bid for them and then the commissioner assigning them to teams, but it would get really messy.
Your best bet would be to do a conference call and then set up a small message board where you post every time a player is purchased and for how much... maybe buy a draft board from one of the vendors so that you can see it and make sure there's no mistakes.
0-3 to 4-3. Worst choke in the history of baseball. Enough said.