The parts catalog (PET) is back up on Porsche's website. I was able to determine the following:
* My headers (part numbers 987.113.103.08 & 987.113.104.08) are actually from a 2006 Boxster, NOT a 2006 Boxster S.
* The 2006 3.2L Boxster S header part numbers are different from the ones that I have.
* The 2007+ 3.4L Boxster S header part numbers are different from 2005-06 Boxster (2.7L) and 3.2L Boxster S.
* The 2007+ Cayman S (3.4L) header part numbers are almost the same as the 3.4L Boxster S headers; only the last two digits are different.
* The exhaust manifold gaskets (between the cylinder head and the header/manifold) have superseded so that the same part number now is used on many Boxster, Cayman and 996/997 911 vehicles. Gasket part number 996.111.107.55 was originally listed for a 3.6L 911 with the X51 performance package, but it is now listed for Boxster & Cayman too. This means that the port openings in that gasket are the same size as the exhaust port openings in the 3.6L cylinder head.
With this information in mind, I drove to the Porsche dealer and compared one of my 987 Boxster headers with the exhaust manifold gasket (part number 996.111.107.55). The openings in the gaskets were an exact match for the port openings in the headers! This means that my stock 2006 Boxster headers will fit the exhaust ports of a 3.6L engine very well.
This raises the question: If the 2006 Boxster 2.7L, 2006 Boxster S 3.2L and 2007+ Boxster S/Cayman S 3.4L headers are different from each other, what's the difference? I would have to see and measure a Cayman S/Boxster S header to get a better idea about that. Given that the port openings in the Boxster 2.7L header are as big as the 3.6L ports, it's entirely possible that the difference between the headers might be something that cannot be easily seen or measured: the precious metal content in the built-in catalyst. This is not as far-fetched as it sounds, since platinum & rhodium are REALLY expensive. What if the difference is in the catalyst substrate type and/or the cell count? The 2006 Boxster 2.7L headers appear to have ceramic substrates. Regardless, I would love to know the tube diameter on the various 987 stock header primary tubes and the header outlet pipe.
2006 Boxster 2.7L stock header primary tube in straight section = 1.65" OD
2006 Boxster 2.7L stock header outlet tube = 2.15" OD
I would welcome similar measurements on known Cayman/Boxster S 3.4L stock headers. That would provide the final piece of the puzzle...