As dry and obfuscated as this is, you probably need to read it all the way through. Much of this is a rehash of claims to authorities made by previous Presidents under a series of Executive Orders collectively called the FEMO E.O.s.
So, has the President taken over the country? Technically, no. What this order states is that the President will be prepared to take over the nation in the event of a National Emergency, but again, this is not a new concept as it already occurs in prior E.O.s.
Part II assigns direct control over the nation's assets to various cabinet positions under that national emergency, but again this is merely a clarification of earlier power-grabs.
So, why now, and for what reason?
Although couched in terms of National Defense, I take special note of Part III, which sets forth several fiscal authorities not previously mentioned in the earlier Presidential E.O.s. The authorities set forth include direct purchase by the government of assets, loans and loan guarantees, subsidy payments, and so forth. These are normally authorities which would originate in legislation in the House, as they involve spending. The end result of this E.O. is that Obama is usurping the spending authority of the U.S. House of Representatives. So, while presented as a proactive plan to deal with the coming invasion of Iran, Part III suggests that the real purpose of this E.O. is to prepare for the coming collapse of Greece and the E.U. by transferring spending authority to the White House ahead of the collapse of the dollar.