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"The President shall have Power to fill up all Vacancies that may happen during the Recess of the Senate, by granting Commissions which shall expire at the End of their next Session." I see no reason why this cannot apply to the Vice President, if Bush so chooses.

One COULD make the argument this clause only applies to appointments made under Article II, Section 2. If that's the case, read the previous paragraph...

..and he shall nominate, and by and with the Advice and Consent of the Senate, shall appoint Ambassadors, other public Ministers and Consuls, Judges of the supreme Court, and all other Officers of the United States, whose Appointments are not herein otherwise provided for...

The Vice President's appointment is "herein otherwise provided for", namely in the 25th Amendment, which states, in Section 2...

Whenever there is a vacancy in the office of the Vice President, the President shall nominate a Vice President who shall take office upon confirmation by a majority vote of both Houses of Congress.

I suppose he could commission an Acting Vice President, but since he cannot formally take the office before confirmation by both Houses of Congress, I don't think that Acting Vice President could be considered the lawful Vice President for purposes of Presidential succession.

In short, I do not think the President could fill a vacant Vice Presidency through recess appointment, at least not without leaving the Speaker as his (the President's) lawful successor. IF the Vice President steps down (not going to happen), and IF Congress refuses to confirm a successor (even less likely, unless the President nominates someone way out there), the President will likely serve out his term without a Vice President.