If Mrs. Clinton had won, then Bush and Cheaney should have resigned before the end of their term as to make Pelosi the firs female President, just to annoy the Democrats.
Since she'd have to give up her seat in the House, I can't see Pelosi accepting the Presidency for just a few weeks. If that had happened, we'd have ended up with either President Byrd or President Rice.
If Bush and Cheney had resigned before Jan 3, she could simply have waited to take her oath of office for her new term after January 20. Or if after January 3, she could have run in the special election.