"On Version 2, how can I style or reposition the view links on the customization widget? The view links appear in a color I don't like to the top left of the image being customized. I want to change their color, font, add space between them and position them below the image or below the controls for each view."
In Version 2 you have full access to the html templates for the customization widget, therefore you can make almost any changes to the widget's html. We use a template language called Twig (http://twig.sensiolabs.org/), which is very similar to Shopify's liquid templates. To access the html templates go to: Use Version 2 / Settings / Html Templates. The code for the view links is in the product.twig template around line 15.