There is no way he “qualified” by Jan 20, 2009. We know that the only person the Constitution allows to act as President right now is Joe Biden.
You make a very valid point. I am inclined to agree with your assessment that it would be the VP who would be President in the case we are discussing. Unfortunately, I don't think anyone but Congress could demand he qualify now, and I don't see that happening. So he will continue to be President.
The Constitution never gives Congress any authority over the eligibility of the President. The only entity that is recognized as having the authority to interpret the Constitution and apply it to specific cases is the judiciary.