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:

   <+q::Send q
   >+p::Send p