Having a brain-fade moment and need help.

I setup a Nikon D70 in a copy stand, with a light table at the bottom in my effort to digitiza MF negatives.
Maybe crude but it seems to work.
However, I'm using a AIS Micro Nikkor 55/2.8 and can;t get it in focus correctly. How should I measure the distance, from the end of the lens barrel or from the film plane?