Hi there. All the info you need is located right here:
Pelican Technical Article: Boxster Engine Conversion Project - 986 Boxster (1997-04) - 987 Boxster (2005-08)
Basically, you can run a 3.4 on your 99, but if you purchase an engine with egas (electronic throttle), then you will need to replace the throttle body with a cable-driven one from a 1999 engine. The details are all in the article / link above, post back here if you have any more questions.
-Wayne