To test the steps #1 and #2 of cleanCART integration, from your Shopify Admin click Online Store > Themes. From the dropdown click Edit Code.
Search for the theme.liquid file. Click on the file to open it in the editor. Make sure the code snippet like below is there:
Search for the checkout.liquid file. Click on the file to open it in the editor. Make sure the same code snippet is there.
After removing the integration, the code snippet is expected to be removed from the liquid files.