Figured it out in case it ever comes up for anyone else. Probably obvious to most experienced rails people but as a newbie it's a whole new concept for me.
I refactored the search results out into another controller and view, which let me use a seperate js.erb file to replace the content of #products while the products controller handles the scrolling endless-page.
So now I have views>products>index.js.erb using $('#products').append and views>results>index.js.erb for $('#products').html etc
I also had to create a results_controller.rb index action as well as a results resource to my route file.
After that both work simultaneously.