EV - you never mention whether you've serviced the hubs on the Fuji's wheels. Why not? What about the bottom bracket bearings?
Have you done a coasting from stop test with both bikes down the same incline? Calibrated the odometers accurately?
I have bikes that give the sensation of riding faster, but in reality, the time differences over the same course are negligible.
Check the hub and crank bearings on the Fuji.