Hi Adam, interesting question, and one which even bunkering companies operating in the US have had trouble getting a complete handle on.
I am not aware of US rules on S% for fuel oil used in ships' main engines to differentiate it from the global Annex VI limit, though such separate limits are in the pipeline in California as per the article you are referring to (
http://www.bunkerworld.com/news/2008/04/71480)
California famously has its own set of standards for fuel used in marine auxiliary engines, but I've not heard of specific limitations in other areas/ports in the US.
There are, however, new US regulations that limits the allowable sulphur content in non-road locomotive and marine diesel fuel (NRLM) to just 500 parts per million (ppm), or 0.05% - a 99% reduction from the previous limit.
They are part of the EPA's Clean Air Nonroad Diesel Rule, and began to take effect from 2007 in the US Northeast and Maine (NE/MA) area.
Outside the NE/MA area, the 500 ppm sulphur limit for NRLM diesel does not apply until 2010.
It seems to apply only to smaller US-flagged marine vessels operating in US waters, (They do not apply to heavy oils used in Category 2 and 3 marine diesel engines) - but it has created confusion about what fuel sellers are allowed to provide. If you want to read more about this, I'd suggest this article:
http://www.bunkerworld.com/news/2007/12/69983