talktobiola Hello
I can login now, thank you!
1/ As I can see that mobile logo is showing correctly now. With favicon, could you try to manually replace the default favicon? /templates/ja_agrivita/favicon.ico
2/ The module Checkout New Products is set to show all latest products now, could you check again?
3/ Jpages, JContent, ... are menu items in Main menu and it looks like you disabled them already.
4/ Here is how the popup of add to cart looks like:

it looks the same as demo site, could you share more details of the difference?