It seems more like he just goes by Youssef as a nickname, though other muslims probably think of that as his "real" name since it is Islamic, while James has obvious Christian connotations.
Plus, it costs a little money and a lot of trouble to make a name change official- a lot of divorced women keep their married names for just such reasons- too much of a pain to change them back.
Now, it may be that he has multiple passports since he may have obtained Syrian passports while he was overseas under just about any name he pleased, and he may have traveled as a Syrian, Indonesia, Malaysian, etc, to who knows where in those 4 years.
There's also no telling who else he might have allowed to use his American id during those four years.
There's just not enough info yet to know how involved he was and how early. He may have been a gung-ho trooper until spending time with some smooth-talking al Qaeda prisoner.
I doubt it owing to his leaving the military and officer's career, selection of Syria earlier on, his Syrian wife, but it's a possibilty. On the other hand, a person who doesn't look arabic would be a valuable tool for both foreign intelligence and for terrorists, and al Qaeda did actively seek out non-Arabs, particularly Americans, because American ID is the best for smooth worldwide travel, and because Americans are the preferred targets. Al Qaeda's plotters really received a timely, convenient gift when the DOD first admitted Muslim chaplains in the 90s.
I wish the press was as curious about the wife as we are.