Hi Jonathan,
Conceptually, the scan tutorial is what you need, not the multi row
tutorial. Hugin can handle two different setups: 1) a 3D scene, while
all images are taken from the same position; 2) a flat 2D object, while
the photos are taken from arbitrary positions.
You shouldn't need to manually tweak any parameters such as the
distance, the optimiser should manage that. From my experience,
however, the optimisation of this scenario is much less robust. I
normally have to add a few vertical / horizontal lines, and it can often
be helpful to first optimise a small subset of images, lock their
parameters, add a few more, optimise, etc.
cheers, Lukas Wirz