Wow! What an excellent report!
I wish all users were like you! Life would be so much more pleasant :)
You are missing one small but important step:
You need to switch to EDAPT Shortcuts from the Edit > Keyboard Shortcuts dialog.
On the video, when you restored the set from the EDAPT Control Panel you even had a prompt to do so, but you probably did not read it :)
When you choose EDAPT Shortcuts all the commands and functions will start responding to key presses.
More info about the set is available here: http://flash-powertools.com/edapt-keyboard-shortcuts-set/
If you'd like to keep using the default set, you can still use some of the multifunctional commands from the menu, but to access the alternative functionality you will need to hold down a key before choosing the command from the menu; for example holding down Alt while choosing Create Magnet Target or Center Marker will create a Centrer Marker.
More info on this is available here: http://flash-powertools.com/understanding-multifunction-commands/
You can also create your own set, but assigning certain combinations in CS is very restricted via the default shortcut dialog, so you will have to dig into the shortcut file itself as described here: http://flash-powertools.com/modifying-the-edapt-cs-shortcuts-set-v-3-and-higher-to-better-suit-your-needs/
Hope this helps!
ps. We think that Flash CS6 is the best Flash/Animate so far, so you have made a good choice.