My interpretation of what would have happened is that Mr. Obama was elected to the office of President by a margin of 365 to 173. Mr. Biden was elected to the office of Vice President by the same margin (365 to 173). If Mr. Obama was not eligible to be elected, it seems to me that the runner-up in the election would have to ascend to the job.
In other words, it appears to me that we would have a John McCain presidency and Joe Biden Vice Presidency.
I think the precedent you’d have to look for is NOT one where the President was removed, but what would happen if the President died before he was sworn in.
John McCain lost. He lost the election. He didn't get enough votes. There is absolutely nothing in the Constitution or in the law that would suddenly turn him from the loser into the winner. If both Obama and Biden are found ineligible to be president then Pelosi is it.