Use JavaScript or Selenium for that Test case. Get coordinates of buttons (getBoundingClientRect()) and compare them. Execute this test case on tons of different configurations.
> * Capitalization inconsistent in top nav
Easy to test. Also add spell checking along the way.
> Popup blockers occasionally stop the App window from opening properly
Selenium?
> Wierd timeout errors clumped around 1:00 am every few nights
You always can shift clock automatically (on Linux).
> Accounting needs to be able to call up weekly income reports
If it is missing feature, then no test case is need until you will start work on it.
PS. If you want to automate your manual testing, you will look for ways to do that. If not, you will look for problems, which are prevents you from doing that.
I wrote example how to execute HTMLUnit tests at build stage because I want that. Almost everybody else says that this is not possible. ( http://vlisivka.pp.ua/en/integration_testing_with_maven_test... )