Here's a thread I remember discussing replacing a 2.5L engine with a 2.7L:
1998 Boxster 2.5 To 2001 2.7 Engine Swap Upgrade
I think that what 'Erlinrys' did covers a lot of what you would do to swap a 3.2L in. I didn't think that the intake from a 2.5L would fit and seal to the 2.7L block, but he said that it worked.
Here's a pic I posted a while back comparing the 2.5L with the 2.7L. To put a 2.7L intake on a 1997 engine, I just had to drill a couple holes for the bolts to line up. In the parts catalog looks like the 2.7L and 3.2L use the same intake parts.
Also note that 2003 - 2004 engines will bring more complications. If you do it, stick with a 2000 - 2002 3.2L or do some serious rewiring to change to a DME 7.8.
I just remembered that 'truegearhead' swapped a 2.7L engine into his 1997 before he got into the twin-turbo 4.2L V8. In his, he simply swapped the cable throttle body onto the 2.7L intake (with some adaptation). That is probably the best and simplest way to go with the 3.2L except I'd want to look at a cable throttle body from a '99 3.4L 996.
PM truegearhead.... I'm bet he'd be happy to give some input.