Absolutely, we will continue working with them making it comfortable for both. It could be the time element here as we've only had the kitten since 1st November but I guess it's always good to get opinions of others.

Thank you:)

Cats see with scent and I guess the scent might be strongest around the anus :')

Work on them associating each other with a positive stimulus. You can slowly let them eat next to each other  (or at different sides of the door first) if you haven't already. Whenever your cat gets angry maybe distract her with playing. 

Or you can take a blanket or something that has your kittens' scent on it and introduce it to your cat while making her associate it with something safe and possible (like playing or food).

I can imagine that its pretty shocking to a cat if all of a sudden there is another species in the house. If you need more tips try to watch jackson in my cat from hell. He dealt with similar (or even worse) situations before. 

Maybe your cats just need more time to get used to eachother, especially your older cat. Give your baby plenty of time :)

This will change once he is neutered, because he will smell different

So my older female cat is about 5 years old and neutered. And the younger male cat is about 5 months and non neutered.

She will walk up to him, take a sniff of his ass then growl and smack him (nothing crazy or violent but it's at least 4 or 5 times a day).

When we 1st got him she was very weird around him, mainly growling and very aggressive towards me and my partner, so we phased in bringing them together but it doesn't look like it's worked.

My older cat gets angry when she sniffs the kittens ass?!?! What on earth is this?