The engine is in the car and it runs, although it is a bit rough. I am assuming that it will take awhile for the ECU to come to grips with the engine change. The more I drive it the better it runs.
So the answer to my original question is: yes the 2.7l engine can be installed without major problems. If the ECU is able to adapt to the engine the only other (minor) incompatibility is the backup light connection.
I will continue to update my experience on the thread for the car at:
Bought a 2000 Boxster S project.