A
Linux distribution [Wikipedia] is a collection of software built around the Linux kernel, like Slackware, Debian, Gentoo, or Red Hat. They all have different conventions and tools, although Red Hat's package management framework RPM is widely used in other Linux distributions. We assume that you are not simply downloading the latest Linux kernel from kernel.org and deploying it along with your own private, hand-picked compilation of user-space utilities (although I suppose that still happens).
So: these 3,000 Linux hosts, are they already out there, and are they running some sort of package management tool or even a well-known distribution such as Red Hat? Or are you going to install and deploy them from scratch?
Would running the Tomcat server in a virtualization environment (e.g. VMware Player) be an option?
I'm not sure I completely grasp which aspect is the main problem here; getting the servers installed and deployed, or designing a scalable infrastructure? Also the stuff about the IPs and ports, is that an installation-time problem or something which needs to continue to work throughout the servers' existence?