Adding to the 'one room at a time' approach, if you don't have the time to clean up something that you already took the time to understand how it works, put a simple comment that reports your wisdom, on the lines of:
 # $jjf is really $objectFromJava.

Now when you return to this code you just mentally s/jjf/objectFromJava/ (Of course in a good text editor this would take a second to actually do, but this is just a simple example).

Another thing: If indentation needs fixing, do it before you even take a second look at the code. This will de-obfuscate things greatly.