Regarding link segments that overlap: there is no good solution at this time, but you could use the code referenced in Extending Dynamic Ports Link Routing Overlapping Issue
In version 3.0 we will provide similar functionality but better. However we’re not quite at the stage for a beta release.
Are you saying that your graph will be planar? Otherwise there will have to be intersections between links. Or is it OK for links to cross each other?
Can you characterize the nature of the graph that you want to display, other than having 1000 nodes? How many links? If the graph will not be planar, what relationships will there be?