Hi @benlauseo,
I guess you will need the list of URLs that won't work anymore (because you've deleted the stores) and then you will need to create the redirects.
You can use .htacess if you are using Apache or you can add the redirects to your vhost configuration.
Another options could be to use the Magento URL rewirte option but I guess you'll get better performance adding the URLs to your vhost configuration.