Clone/Mirror Live Linux (Debian) Server

I've probably read every serverfault article on this matter, but none seems to answer my specific question or they seem like dated methods.

I have a live running debian (Lenny) system on Dell PowerEdge 1750 hardware. It's running mysql 5.1, Apache2, and ISPconfig. The system is a few years old, and has a lot of dated packages and software. We just want to make sure we have a cold server ready to go in case something happens.

My goal is to convert it over to newer hardware and software in the future.

I have been instructed to not shutdown the system. Clonezilla will not work since it requires offline, and rsync and dd really don't seem to be cloning tools, more like syncing tools. I tried to get mondo working, however mindi (part of mondo) seems to be crashing when it tries to create the ISO file... which I do not even want, I just want an img or gzip or just raw files.

Does anyone know any other free tools that would allow me to clone/mirror a live running system to another system?

The solution I'd use for taking a point-in-time snapshot of a running system is the (free) Idera/R1Soft Hot Copy product. Using this, you can take a clean snapshot and rsync the entire copy (or portions of the copy) to another system.