ORIGINAL Q: I\'m wondering if anyone has had experience of migrating a large Cobol/PL1 codebase to Java?
How automated was the process and how main
You are speaking of reengineering. The good thing is that a lot of people worldwide tries to do this. The bad thing is that there are a lot of problems concerning legacy applications reengineering: starting from missing sources and up to complex algorithms from compiler construction and graph theory fields.
Idea of automatic translation is very popular, until you will try to convert something. Usually the result is awful and unmaintainable. It is more unmaintainable than original complicated application. From my point of view, every tool that allows automatic translation from legacy to modern language is very marketing oriented: it says exactly what people want to hear "translate your application from ... to Java once, and forget!", than you are buying a contract, and then you understand that you very tightly depends on the tool (because you can't make any change to your application without it!).
Alternative approach is "understanding": the tool, that allows you very detailed understanding of your legacy application. And you can use it for maintenance, or for documenting, or for reinventing on new platform.
I know a little about Modernization Workbench history before Microfocus bought it last year and moved development to another country. There was great number of complex analysis tools, and number of supported target languages (including Java). But no client really used automatic code generation, so the development of generation part was frozen. As far as I know PL/I support was mostly implemented, but it was never finished. But still you can try, may be this is what you are looking for.