I think the issue is that the '03 996 motor has variocam+, but the '03 986 only has variocam. fortunately, the 7.8 dme in the '03 986 is up to the task - you just need to run some wires and reflash the dme with an oem '02+ 996 flash. info here ...
Porsche Boxster Engine Conversion Project - 986 / 987 (1997-08) - Pelican Parts Technical Article
specifically:
"The 2007-08 Boxster engines were the first of the series to get Variocam Plus (variable valve lift). The Carrera 996 had Variocam Plus since the introduction of the 3.6L engine in 2002. The 7.8 DME used in the 2003-06 Boxster didn't control variable valve lift, and there are no pins or wires in the engine harness to control the mechanism. Therefore, you need to add the wires into the engine harness when performing this installation. Pins A1 on both valve lift controllers connect to a 12V source in the harness: use the 12V supply for the variable valve timing solenoid. Pins A2 on the controllers connect to DME connector pin C1 for cylinders 1-3 and pin C26 for cylinders 4-6."
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