I believe in your userdata script you can write a line to download a Python script from S3, then proceed to execute. Don't quote me on this since I don't use userdata.

However, note that userdata will only run once at launch time. If you ever need to re-run userdata, you have to stop the instance, remove the userdata from settings, and then add again. YMMV.

I do the Python way when launching a beanstalk instance (basically cloud init).