For anyone who is interested, I've created a VERY basic open source Mod Manager for SpinTires Mudrunner. The method it uses to store and activate the Mods is different then how JSGE stores the Mods. It uses a method I picked up in an earlier post. Thanks to @Tattoo for pointing it out.
This is just the first iteration, so I am sure you are going to run into bugs.
If you are just interested in running the program:
Just unzip the folder somewhere. Since this was built with .NET, you'll need to have the .NET framework 4.6.1 or higher.
If you are interested in the source code, you can clone it from the main project page.