There is one pretty important thing to keep in mind as we await Judge Vinson's decision on the United States' Motion to Clarify.
That is, even if Judge Vinson clarifies that his declaratory judgment indeed has the force of an injunction, and thus that it precludes the United States from enforcing any part of the ACA, he is still apt to grant the United States a temporary stay (for instance, of 5 days) to seek a stay from the Eleventh Circuit. I hesitate to say anything is truly "likely" in this litigation odyssey, but such a move does seem probable. It would be a standard courtesy to the United States, especially in light of the practical complications raised by an immediate halt to implementation highlighted in the DOJ's filings.
So, even if Judge Vinson's ruling goes against the United States, the DOJ will likely have time to seek a stay at the Court of Appeals before it must completely "cease and desist" implementing any part of the Act.