If the column distance gives you the distance between the negative and the paper, then you have the have the quantity d_o + d_i, when d_o is the object distance (negative to lens) and d_i is the image distance (lens to paper). But perhaps the column distance measures some arbitary point on the head. (This also neglects the separation of the principal planes of the lens, but that shoud only be a couple of mm.)
The focusing equation is 1/d_o + 1/d_i = 1/f, where f is the focal length. Using the equations for magnifcation (e.g., d_i = f(m+1)), and some algebra, one can obtain the equation:
d_o + d_i =f/m (m+1)^2 = f (m + 2 + 1/m)
So from the column height, hopefully a measurement of d_o + d_i, you could solve the above equation for m for both print sizes, then use the (m+1)^2 equation to calculate a new exposure time. Obviously the above equation is not so easy to solve.
Possible approaches: 1) measure the lens position and not bother with the above equation, 2) program a scientific calculator or computer to solve the equation, 3) measure the film and prints to obtain m, 4) use a light meter, or 5) test strips.
To measure the lens distance accurately, you could just mark the optical center line on the baseboard and extend a tape measure from the lens to that point. I would't worry about the nodal points of the lens -- measuring to the aperture or middle of the lens should be sufficiently accurate.