Maybe I should have mentioned this in my answer to your original question, but this requirement is much too case specific to be a good addition to a general purpose editor such as yEd.
Moreover, in the general case it is not possible to arrange a graph according to your requirement (suppose you have nodes a,b,c with dist(a,b)=100 and dist(a,c)=dist(b,c)=1). The fact that the distances should be whole numbers complicates the problem even further.
That said, should you already know an algorithm that arranges graphs according to your requirement (assuming a set of distances for which a solution exists), you could implement a custom application with your algorithm using one of the yFiles programming libraries. Please visit the yWorks website for further information on yFiles.