Furthermore, I was assisted by Jim's choosing which source directories to use. That really cleared up a lot of the mess.
I ran Emma's code coverage on JUnit tests using Eclipse of this clean build, and saved the file. This will serve as a template against my version, so that I make sure that I'm not breaking something which wasn't already broken.
A number of tests failed. Will include complete report when I find a place to upload it.
EDIT: Here it is.
The original post can be found here: https://anterence.blogspot.com/2010/05/emma-coverage-report.html