I would like to start with the Wowza EC2 AMI, make some changes to the instance, then build a new AMI with my changes to the instance so that I can start new instances with my changes/updates already in place (scripts and applications installed + security configuration to the Operating System).
Q: Will this break the Wowza configutation in any way?
Build an Amazon AMI using the tools provided by Amazon.
Install the Sun Java JDK version 6 update 13 (or more recent version if available) and the most recent version of Wowza Pro 1.7.0 (I would also suggest you install the most recent patch from here https://www.wowza.com/devbuild.html).
If it is just Wowza configurations that you are trying to preserve, using a “start-up package” might be the way to go. Take a look at the Wowza EC2 Guide. You can mix these startup packages and add your own scripting, install jar files, etc. You do your work in the package, zip it up, and startup an instance with it.