I think the trig is as follows:
width_of_big_rectangle = width_of_little_rectangle + 2 x distance_between_rectangles x tan (horizontal_angle_of_view / 2)
eye_relief = distance_between_rectangles * width_of_little_rectangle / (width_of_big_rectangle - width_of_little_rectangle)
The aspect ratio of both rectangles should be the same as the aspect ratio of your film.
You can use any unit for the distances, provided you use the same unit throughout. The angle unit should be as required by your calculator (or trig tables) - probably degrees.
Parallax is an issue for any camera where the viewfinder does not see from the same point as the lens (i.e. not in LF cameras and SLRs but pretty much everything else). If you mount the viewfinder directly above the pinhole (i.e. not to the left or right of it) then ant least you won;t have to worry about parallax in the horizontal direction. If necessary you could use multiple horizontal wires in the big rectangle to demarcate the close and far focus frames.
Bill's suggestion is probably easier though