Gee, I hope you made a snapshot of the VM before trying out the install? ;-)

Well, since you ask I'm guessing that you didn't and that you have learned that point the hard way now but too late. My sympathies. :-(

The bork effect can happen if you've gotten the wrong ownership for the xkb files. If you have the console working, you could try running the following command:

$> sudo apt-get install xkb-data

Before that, you could always try restoring your xkb files with my install script:

$> ./install-dreymar-xmod.sh -r 1

You don't have to clone the VM! There should be a snapshot function which is like an incremental backup in that it can rewind your VM state to one (or several) set point(s). Always do that before trying anything brave. It's one of the reasons I actually prefer Linux VMs over real Linux installs these days. (Not sure if it's free to use with VMPlayer? I use VirtualBox these days as it's actually free.)

XKB is a beast. Good luck with it, hehe. But basically what you can do is swap around key names in my symbols/extend file. That'll change the lv5 up definitions of keys without changing anything else, and should be what you're looking for.

Example: A snippet from my extend file.

    key <AC06> { symbols[Group1]=[ NoSymbol , NoSymbol , NoSymbol , NoSymbol ,
                   Page_Down            , Page_Down             , // PgDn
                   Page_Down            , KP_Next              ], // PgDn
                 actions[Group1]=[NoAction(),NoAction(),NoAction(),NoAction(),
                   Redirect(key=<PGDN>) , Redirect(key=<PGDN>)  , // <PGDN>
                   Redirect(key=<PGDN>) , NoAction()           ]
               };  // H
    key <AC07> { symbols[Group1]=[ NoSymbol , NoSymbol , NoSymbol , NoSymbol ,
                   Left                 , Left                  , //  ←
                   KP_1                 , U21D9                ], // KP_1 ↙ ⇙
                 actions[Group1]=[NoAction(),NoAction(),NoAction(),NoAction(),
                   Redirect(key=<LEFT>) , Redirect(key=<LEFT>)  , // <LEFT>
                   NoAction()           , NoAction()           ]
               };  // Cmk N

If you were to swap <AC06> and <AC07> in the above, your Ext+H would become Left and Ext+N would become PgDn. (Unless you use the Ext+AltGr mappings, don't worry about that bit.)

Not sure what you mean by mapping colon to O. On the Extend layer? See above. On the main layout? You'd have to look in the symbols/colemak file.

You're wrong: A snapshot saves the whole shebang. Only saving the virtual RAM and not the virtual disk state would be pretty pointless and cause bad errors.