As I want to install Jenkins (ex-Hudson) to operate my continuous integration processes on AWS Beanstalk, I need a custom AMI because some parameters in Tomcat & Linux h
You should be able to create a customized AMI from a running instance as long as you delete /opt/elasticbeanstalk/srv/hostmanager/db/hostmanager.db on the instance before building the new AMI. I keep seeing people say "it can't be done, you need to start a clean instance outside of Elastic Beanstalk" and that's bunk. I've done it.
A full write-up of what I've done to customize my install is here: http://stormerider.com/blog/2012/08/16/building-an-ubuntu-ami-with-elastic-beanstalk-support/ -- some of it may not apply to you, some of it may.