I ended up using the batch files simply because I've been using them for years and I'm comfortable with them. More a lack of experience with AHK than anything; although I can read your script and it makes sense to me, I've done similar things with batch files before, and once you gave me the idea I just ran with it.
A note to readers though, if you use batch files for this and for some reason your batch file doesn't fully execute, you'll have to go in and manually recopy files to get everything working again (which is why I made backups of the cfg files in a separate folder). Plus Skurdt's method has the advantage of being path-independent, whereas mine would require adding a new variable to Windows for the path to the cfg files unless you hardcoded the path right into the batch file like I did.
3D Arcade Command Line Switches
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