I have made a totally changed Category Layout, where I used the Modal for the popup of the Category Items -> Item

This was working flawlessly untill 2.6.6 update (from 2.6.5) - I now need the modal.js loaded, and modal.css and also the Javascript - all 3 things in the header.

Any way of letting this "back in" - without having to hardcode it in the template ?

I am afraid not, you need to add