I'm running a 2005 3.6 in my 1998 Boxster with the original 1998 5 speed tranny. It's been driven over 47,000 miles without a hint of any issues. You will need a 7.8 DME to replace your 7.2 DME. You cannot reuse the 996 engine harness, you must add wires to the DME's connector 3 to control valve lift. You must fabricate tubing from the air cleaner to the 996's throttle body and replace the MAF tube and sensor.
Not an all inclusive list, just some of the PITAs.
http://986forum.com/forums/boxsters-sale-wanted/36540-sale-3-6-boxster-$20k.html
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1998 Boxster with 7.8 DME, 2005 3.6 liter/325 hp, Variocam Plus, 996 Instrument panel
2001 Boxster original owner. I installed used motor at 89k.
1987 924S. 2002 996TT. PST-2
Owned and repaired Porsches since 1974. Porsche: It's not driving, it's therapy.
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