Hello Dave,
if the numbers don't match, the engine doesn't belong to the car. If the engine was rebuilt by Porsche it has to have the digits AT in the serial number, which this engine obviously doesn't have.
Engines that were rebuilt by Porsche at this time don't have handpunched serial numbers. In general they have used new engine blocks for the rebuilds, because of the coating problems of the cylinder walls.
I think it's a good idea to ask Porsche UK for some support? Maybe they can help and give you validated data on the car.
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Hello FoxRvrBox,
there are some infos about the serial numbers and IMSB versions on this site:
Pelican Technical Article: Boxster Intermediate Shaft Bearing Replacement and Upgrade (IMS) - 986 Boxster (1997-04) - 987 Boxster (2005-06)
Caution: the description of how to change an ISMB is outdated. If you have an AT engine, nobody can tell what ISMB is used.
Regards, Markus