I am thinking of buying this plugin. But from what I understand I would need to manually add link for each store for each product. I have more than 3000 products so adding link for about 10 stores for each product would take forever.
Is there option to do this automatically? Maybe using import plugin or something?
You can use any import plugin you like. When you create affiliate products they get created as External Products in WooCommerce, so there is a field for the external url.
Additionally, when importing, you can add the other comparison URLs. See our support area for guides on this for importing.