Do NOT change your currency settings as described in the “Sectioned Themes” post, as this will break any currency selector you might have installed in your store.
Make sure to keep your store’s currency settings WITH the span class tags, like this example:
HTML with currency: ${{amount}} USD
HTML without currency: ${{amount}}
To fix the issue where the span class appears in the shipping calculator rates estimates:
Go into the shipping-calculator.liquid snippet you made earlier and find {{price}} (with double curly braces).
Change that to {{{price}}} (with triple curly braces).
(In Handlebars, which this snippet uses, {{price}} will be HTML-escaped, but {{{price}}} will not.)