I've tried de-clicking an AIS Nikkor. Removing the click-tab also removes any and all resistance on the aperture ring, so it's free to just turn on its own. In addition to feeling like garbage and occasionally making a fingernails-on-chalkboard noise, the aperture ring moves on its own when attached to the camera since the metering coupler on the camera is spring-loaded. I took some pictures of the lens parts below so you can see how de-clicking/re-clicking the aperture ring would work in theory. I don't know if all Nikkors are built like this, however.
Regarding the exposure discrepancies, I too would be interested to know which camera was used? The F5/F6 are supposed to have shutter monitoring systems that makes corrections as needed. My guess would be that the manufacturing tolerances in Nikkors are not up to your standards, Mr. Stone :P
There are lots of "T-stopped" cinema lenses for F-mount bodies, but they appear to be upwards of $3K each.
I found the apertures on Nikkor lenses are very accurate. I have no complain. I found even with the F5 the shutter speed accuracy still not very good.