I evaluated some dependency-analysis software called Sonar-J which turned out to be excellent for this kind of work. Don't know if that was one of the ones you looked at? Analysis seemed quite fast, can be done with a mix of class files and source, and is displayed in a flexible and intuitive arc-diagram. I understand the urge to dig into the raw data, but I have to say this software quickly turned up a few unexpected things in my code base: I was very impressed. The one drawback is that the community-license (free) copy may not handle the number of classes you have, and the price is not negligible.