Trying to automate a manual procedure in place currently. This is on a Windows 2008 server.
Is there a method to create a self extracting (.exe) zip file from a commandline/batch file?
No, not without additional software installed on the machine, such as WinZip or WinRAR or 7-Zip, etc.
If you do have one of these other pieces of software, then you'll need to reference its command line options.