Save site as template link is missing

I was trying to create the site template from a site where the "Office SharePoint Server Publishing" feature was activated for some reason. But the issue here is after activating the "Office SharePoint Server Publishing" feature the "Save site as template" link from the "Look and Feel" section of site settings is missing.

I understand that its disabled because the functionalities part of "Office SharePoint server Publishing" can't be included in the site template(.stp) file. But i have applied lot of customization which are not related to publishing feature, I will be requiring those changes in a template file.

So if we have the core template we can apply the publishing related changes on top of the site created with the core template.For that we need the core template...we can still get the template by calling the "_layouts/savetmpl.aspx" page from the address bar. We should also make sure we will be applying the publishing related changes on top of it.