You were very close to the solution of your problem ;)
Control Panel -> Regional and Language Options -> Languages tab -> Details...
There, you can edit the hotkeys to change input languages. If you press the Change Key Sequence... button, you will be able to change (disable) the hotkey which switches keyboard layouts (that Ctrl+Shift combination you mentioned).
Yes, there is a way to use the MSKLC custom layout in Windows 8.1. It's not more than a workaround, I'd say, but it works:
Go to Control Panel → Language → Advanced Settings
Under Switching input methods select Options and then Advanced Key Settings
Here you can assign a shortcut that directly activates your custom keyboard layout (in combination with a language, so if you want to use the same layout with different languages, you need one shortcut for each combination in order to swap between these).
BTW: I suspect that the reason, why some people report that MSKLC works with Windows 8 is that they have only one keyboard layout or one language installed so that the system automatically uses the custom layout and hence there is no need for all of the above.
Best Answer
You can disable the sequence Ctrl + Shift in Windows 8.