My ctrl key seems to mimic my Command key for most of these command and not do anything in other cases (Firefox & Word). Is there some setting I need to change?
I'm using these keybindings in Firefox right now, without any custom config (other than mapping caps lock -> control). Go to the URL bar and hit control-a and control-e; do they work? Type a few words of a reply comment, and in the comment text field, try control-a and control-e; do they work?
Neither of those programs use readline. I map ctrl-e to end of line in Word because I use it so habitually. Safari uses these shortcuts as does terminal.