Nice summary of the challenges in improving on the stock intake design Radium. From my rough calculation, a 2.5L 6cyl motor only requires a 2" ID intake to achieve max VE at redline so I don't have heartburn over the stock design. If I jumped to a 3.4L motor and exhaust I would certainly need to re-tune the intake. No well-tuned intake would be complete without a carefully placed helmholtz resonator to cancel the acoustic pressure wave that would otherwise certainly foul your MAF sensor readings. Bigger and smoother are just the tip of the iceberg in a performance-tuned intake design.
A useful resource for getting the math right:
Volumetric Efficiency (and the REAL factor: MASS AIRFLOW), by EPI Inc.