Your comments

However the code will need to be executed upon creation/opening of a new file which will not have the new styles implemented.
This is tested in Canary Chrome and does not cause problems with scrolling multiple panes.
You have an e.preventDefault in the js of your header but it might be a different event according to Chrome

// Keyboard shortcuts
$(window).keydown(function(e) {
if (e.metaKey) {
// e - snapshot
if (e.keyCode == 69) {
$('#fsnapshot a').trigger('click');
e.preventDefault();
return false;
}
// s - save
else if (e.keyCode == 83) {
window.editor_app.save();
e.preventDefault();
return false;
}
// o - toggle file manager
else if (e.keyCode == 79) {
var showing = false;
if ($('#fileManager').is(':hidden')) {
showing = true;
}
$('#finderTag').trigger('click');
if (showing) {
$('.elfinder-cwd-view-icons').focus();
}
e.preventDefault();
return false;
}
}
});

Ran out of time to write more but:
changing e.metaKey -> e.ctrlKey might work
The demonstrative jsFiddle works for both Windows 7 + 8 with google chrome. provided you focus on the Result box by clicking on it. Then proceeding to CTRL+S
This does not work using Google Chrome on Windows 7 or Windows 8.
CTRL + D for delete line works though. But Google chrome overrides the CTRL+S implementation by asking if I wish to save the webpage.