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I am thinking of something similar. I think I will indeed attach the wedge to the bottom of the glass to be in contact with the film, rather than above the glass like the original. But rather than let the glass be loose and depend on its weight for pressure, I will put thin black paper under the film to press it upwards. The glass is not heavy enough to do much, so shimming under the film is probably the best way to go with this design. I think I will have to filter the light to reduce exposure rather than increase, so I can lay the ND filters on top of the glass and keep the time to the original 1 second. Longer than that and I start getting into reciprocity failure. I could also replace the original spacer pictured above with a piece of processed film, which would make the gap smaller. The spacer serves no other purpose.
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Or you could increase the spacer, to fit a standard piece of glass in the original channel. Get the glass chamfered so the film will slide under it. Tape the wedge underneath. I don't think you need to be critical about contact with the step wedge, not like you care about the sharpness of the image.
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Well, I just ordered a piece of .5mm thick glass as you were typing. I actually got two types: soda-lime and alkali free. I will see which is the most colorless when they get here.
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Looking at that design I think it will work fine in its original configuration. There will be no bleed around the edges of the step wedge (so perfect contact is not needed). There is potential for a small amount of bleed between the steps, but I suspect it is insignificant.