I tidied up my code a lot, and combined the 8 or so different versions of the programme into one that takes command line options.
I made a few more options for the data output, I tried removing all leaf nodes, so it would only display core nodes, but this had little impact in clarifying the data. I tried eliminating the first arbitrary number of nodes in each hop, but the graph would break up before there was any significant improvement in clarity. I also allowed it to remove any hop that never had an rtt less than 35ms, in order to remove the foreign nodes that had creeped in, though this led to a lot of false positives.
I also managed to get gephi to produce an ASN graph, though my solution was pretty clumsy. I saved the graph in gephi, edited the file and reopened it..
I also made a graph with LGL. Gephi is coping with the size of the graphs however, and does give a lot more control over how the data is represented.