What you've got is a mess of hacks, one piled atop another, and trying to use an AutoHotkey script to translate paths is just going to make that even worse.
What you need is to rip out that nonsense and do a proper Cygwin install, which will give you a proper terminal emulator in mintty, and a proper Unix shell environment which has already had a lot of the work done to make it play nicely with Windows -- for example, there's a utility,
cygpath, which is included by default with Cygwin, and which accurately translates paths in both directions.
I'm not sure why people seem lately to be so hot on Git Bash over Cygwin. Judging by the page you cite for the process you followed, installing Cygwin is actually less effort than piling up the hacks, and you get a better experience out of it.