From:
http://www.pelicanparts.com/techarticles/Boxster_Tech/11-ENGINE-911_Engine_Swap/11-ENGINE-911_Engine_Swap.htm
The Boxster 2001 cars are by far the most flexible in which engine you can install in them. The 2001 cars still have the 7.2 DME installed, but most of the other systems of the car were upgraded in anticipation of moving towards the 2002 CAN bus system that integrates various electronic systems on the car. With the exception of the anti-lock braking system, the proper CAN bus systems are integrated into the 2001 chassis and allow the easy installation of the later 7.8 DME. As a result, you can install any 1997-08 Boxster or 996 Carrera motor into these cars without too much difficulty. You can swap in any replacement engine of the same displacement from 2000-02 without having to remap the DME. (for example, a 2001 3.2L Boxster with a blown motor can accept a 2002 3.2L engine with no remapping needed).
To install a Carrera 996/997 3.6/3.8 engine or a 2003-08 Boxster/Cayman engine into one of these cars, you need to purchase a new 7.8 DME and then slightly modify the pinouts on the DME connector. In addition, you need to modify the Boxster engine wire harness, as the camshaft position sensors are located on the opposite ends of the engine than on the 5-chain early motors. All of the systems on the car should work normally with one exception: the cruise control will not work properly with the later 7.8 DME unless you upgrade your ABS system as well (swap out the ABS controller and connector).