Yes, you can do it with AutoHotKey. I tried it a few years ago but didn't really get on with it. I think it might have caused problems with some keyboard shortcuts I use - a lot of my emacs shortcuts are designed for activation with one hand pressing modifier keys and the letter key.
Anyway, just use the < and > modifiers to indicate left or right Shift specifically. For example, assuming QWERTY:
No, sorry - the bit from the article that was in my mind as I replied was forcing one to use the opposite Shift, because I'd tried that myself. I didn't think about the use of Shift as a key on its own (I really wouldn't get on with that myself as I tap the meta keys a lot while I'm thinking).
Anyway, just use the < and > modifiers to indicate left or right Shift specifically. For example, assuming QWERTY: