Big Mess--How to use Git to resolve

I want to use Git, I have had read documentation installed on my local machine, then looked at my mess of code and don't know what the hell to do.

I have a Perl Web Application, several hundred programs, templates, configuration files.

Companies buy my application and I host it for them.

I have 40+ clients

Each client has its own unique installation of the software on my web server.

Some clients have customizations of the code, some have version 5 of the software others have 5.2, 5.5 etc.

This sucks.

My goal is to pull all the different versions in, put them all together, and create a master version of the software that runs for all clients.

There will still be some files that are completely unique to each client (style sheets and logos for instance).

I can't figure out if I should start with my oldest version of the code or the newest, I haven't really found in the documentation how to start with different permutations of the code in a repository. Everything I have found assumes you start with one set of code, then make changes. I have multiple variations and need to get them consistent.

I expect to use all of 2012 getting this put back together, but I have to start. Does anyone have any suggestions on how I should set Git up to do what I need?

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