Can I determine how the Flashback trojan infected my machine despite disabling Java? Apple's update on April 17, 2012 detected and deactivated the Flashback trojan.

Yet two weeks ago I had following the instructions here. After concluding that my Mac is not infected, I disabled Java.

I don't understand how Flashback could have sneaked in, especially after my guard has been up after an Arstechnica article, but that no longer matters.

How do I find out what kind of damage might have already been done? Will one of the log files contain a trace of what has happened?
I'd be surprised if the logs told you anything useful. 

If you're concerned, you could install one of the free AV products for the Mac. Do a full system scan to ensure that all traces of the trojan have been removed.