Thanks to the poster and the answers so far; these helped me solve my similar issue: I have keyboard shortcuts on my desktop PC's text editor that use Ctrl+Alt+..., and I wanted to be able to use them when accessing the machine remotely.
With this AHK script, I type Win instead of Alt and I'm able to accomplish the commented commands below. Now regardless of which PC I use to access the remote desktop PC (i.e., when home or traveling), I can use my shortcuts (and Win is pretty near Alt). Here's my AHK script:
;Send Ctrl+Alt+Left keys when user types Ctrl+Win+Left
;Send Ctrl+Alt+Right keys when user types Ctrl+Win+Right
;Send Ctrl+Alt+Up keys when user types Ctrl+Win+Up
;Send Ctrl+Alt+Down keys when user types Ctrl+Win+Down
;Send Ctrl+Alt+Shift+Left keys when user types Ctrl+Win+Shift+Left
;Send Ctrl+Alt+Shift+Right keys when user types Ctrl+Win+Shift+Right
;Send Ctrl+Alt+Shift+Up keys when user types Ctrl+Win+Shift+Up
;Send Ctrl+Alt+Shift+Down keys when user types Ctrl+Win+Shift+Down
Note, I use "Apply windows key combinations...On the remote computer" in Remote Desktop Connection, so I run this script on the remote computer.
While there are probably more efficient AHK ways to do this, the above works for me. Hope this helps someone else, too.