Dot was getting stuck in the second “network simplex” invocation. Here is a command line that should give you output in 3 to 5 minutes (+/-):
dot -Tpdf -Gnslimit=2 -Gnslimit1=2 -Gmaxiter=5000
(see Where does generating the graph take most of the time? - #4 by ethuo for more on this)
I think SVG will work better than PDF.
You may want to consider reworking your nodes to get them narrower (by eliminating text or adding newlines).