Managing a substantial Python (or Ruby) project is easier than you'd imagine because there is so much less code and configuration. There is also less "architecture astronautism" with all the layers of abstraction hiding what's really going on. You can still have some of that, but in my experience, it's pretty rare.
The biggest issue when stepping outside the JVM (in my opinion anyway), is dependency management. The libraries you want may often not be pure Python or Ruby, but have C/C++ stuff in there too. This can make setting up an environment on multiple OS platforms tricky, since you need to install (and maybe even compile) all that stuff. There's something to be said for throwing a jar on a classpath and being done. However, I suspect you'll find these languages cut development time so much that you're still ahead of the game after burning a little extra time installing some dependencies.
Performance-wise, both Python and Ruby are probably "fast enough", certainly when developing apps that are not used by large numbers (i.e. web-scale numbers) of people. Internal apps in particular run perfectly fine with no exotic caching, partitioning, parallelization, etc... There are also plenty of companies out there that operate very busy, successful public websites with both Ruby and Python, so in general, the performance should be the least of your worries. Obviously, if you're looking to do scientific simulation or some other compute-heavy work, your mileage may vary.
Editors are another thing that trip people up going to Ruby and Python from Java. Take my advice: ditch your IDE and use a regular text editor with syntax highlighting. There's no way I write Java code without an IDE, but for languages like Ruby and Python, it's not necessary and the IDE just gets in the way. Keeping an interpreter window open when dealing with a library you haven't used before is far more productive. You can create some fake classes, try out some methods, and once you have a feel for the thing, move over to your editor and code up what you want. That beats the pants off autocomplete any day (and the inevitable compile, run, test cycle that goes with it).
EDIT: Oh, and learn JavaScript if you don't already know it. It's only going to get more important.