If you're just making changes for your own site, rather than intending to develop a new theme to be shared with other users, I'd just alter the theme.php and style.css files as required - and, of course, ignore any prompts to update the theme if they appear.
If you do want to make your theme truly independent of the original Sky theme then I would follow all the steps in the Theme tutorial.
(Regret haven't made time to check the changes in your json file.)
I will go, for now, to change te files in the themes\sky folder, and hopefully I do not forget I manually changed something in `theme.php` when I press UPDATE some time in the future .....