Hello, updating this thread, the number of products in your Shopify store should not affect the integration process. If you or anyone else is experiencing the same issue, please reach out to us at [email protected] so we can look into it and troubleshoot directly.
In the meantime, here’s our full guide on connecting Shopify to Funnelish and setting up product automation: 
https://community.funnelish.com/t/how-to-connect-shopify-to-funnelish-and-set-up-product-automation/9914