Hello,
1. You are right, this will have impact on SEO. But in this case, we can do nothing, because of even with default Woocommerce theme – Storefront you will have 404 page using the plugin. I would recomment you to contact plugin author to make the button work correctly with your custom links and Storefront theme.
2. Only permalinks and custom css were changed.
3. Looks like after changing theme on site to the default and back, some widgets changed their positions. You may set widgets to appropriate areas in Appearance > Widgets. Sorry for the inconvenience.
Regards