The engine itself, does not need to be an automatic. There are some peripheral items that you can swap, such as the wiring harness and the plumbing. Some minor vacuum hose changes. Flywheel will need to be from (or new for) a 3.2 automatic
There are other considerations regarding year for the sensors, DME/ECU, throttle, etc.
Read this yet?
Porsche Boxster Engine Conversion Project - 986 / 987 (1997-08) - Pelican Parts Technical Article
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