I am still tweaking my MPGuino setting for injector ms/gal, so I can only go tank to tank for accurate results. I have the vss pulses per mile dead on. Last tank was over 400 miles and I was within 1 mile between the odometer and the guino. My commute is out and back the same route on 2 lane roads. Approx. 90 miles of 55mph hwy and 15 miles of 35 mph city total. I will finish this tank with the hose off, and then put it back on for the next tank.
With our ZETEC engines having no egr, and using the VCT for emissions purposes, I wonder if the results you are seeing are a combination of the sensors and the cam timing.
I was thinking of something like this for tweaking the O2 sensors for trying to lean things out:
DIY Dual O2 Sensor U-Solder Kit (EFIE)
Having fun yet?