The settings you mention all sound fine, but the I believe the Flex War file may be what you referred to as the flex-tomcat files (specifically the one should be called flex.war from the install folder).
You don't need to deploy the flex.war file to JBoss manually, when you create a project, you just select the file in the wizard and it is extracted and used as a template for the new project. In fact, it may cause a port conflict with your project if you do deploy manually it (unless you tweak some of the config files), so it's probably worth removing it from the deploy folder if you did put it there. The other file, flex-admin.war, can stay without causing issue.
The closest to a tutorial that I am aware of is if you search "New Flex Project" in the help system, it talks about what each of the options should be when creating LCDS projects.