I have been reading this thread, and see that no one has come up with a solution for control, alternative and shift modified keystrokes. But someone has mentioned that saying "type" followed by a keystroke command, such as "control four", will trigger to the right shortcut. This brought me to a solution.
Instead of using the windows speech recognition macros you can use Vocola 3. This extension has a function called HearCommand("Text string"); this command tells speech recognition that eat just heard the string defined in the command. It has also other usefull commands that alow for example dictate to chat.
Originally Posted by Beginning of my script file
# Voice commands for Star Trek Online gameclient
# Disable dictation on load to prevent keystrokes that are not commands