I finally had the chance to do abit of testing with a friend's 5D.
First thing's first:
it's near impossible to get everything aligned.
Slight variance in positioning due to things like the release plate not being exactly at the same spot...The two files are cropped down abit to match up in terms of positioning.
Next is colour temperature variance...not sure if the colours between different units of 5D mkII cameras are different but one camera was definitely more magenta, one was more on the green side. The modification of the glass definitely plays a role here. The difference in colour cast probably has an effect in the contrast of the image.
focusing variance was also an issue. out of the 10 different series of shots we did this was the most close series of pictures we had in terms of focus from two different cameras using the same lens
85mm f1.8 wide open
focus is supposed to be right smack in the centre of the picture, on the right edge of the grey speckled pillar.
To compensate for focus error I guess you'll have to compare detail of the closest object to the furthest object.
Nonetheless, certain interesting details can be observed when zoomed in to 400%, visible at 200% too.
Would love to do a stricter test to see the effect of this modification, when I have the time
full size (slightly cropped) jpegs here
Processed in ACR, with sharpness set at 10 radius 1.0, noise reduction at 2
http://superhyperreal.com/compare1.jpg
http://superhyperreal.com/compare2.jpg