Oh wow, I refuse to pick! Your entire list is fantastic! As are your sons names, [name]Rafferty[/name] is pretty high on our own list.
Ok so if I had to choose I would go with [name]Penelope[/name] [name]Jane[/name]. Its just so sweet and classic, flows really well, has a nice vintage charm and would sound great with her brothers. Not to mention, [name]Penelope[/name] is our number 2 girls name, and the combo I currently have for it is [name]Penelope[/name] [name]Jane[/name] Eflyn (called [name]Nell[/name], occasional nn [name]Nellie[/name]-[name]Jane[/name]) since [name]Jane[/name] is my middle name. So obviously I love how [name]Penelope[/name] and [name]Jane[/name] sound together. I love love love [name]Penny[/name] too, but unfortunately for us my [name]MIL[/name]'s dog is called [name]Penny[/name] so thats out, although I love [name]Nell[/name] just as much so I guess it saved us from having to make a difficult decision between [name]Nell[/name] and [name]Penny[/name]!
Second favourite may be [name]Clara[/name]. I like [name]Clara[/name] [name]Beatrix[/name] a lot, but I adore [name]Clara[/name] [name]Primrose[/name]. I have a soft spot for [name]Primrose[/name] since its my great-aunts name, plus I think its just so underused and unexpected. I know a sweet little 1 year old [name]Clara[/name] with curly brown hair and big brown eyes and the name is so cute on her. So yes another great choice.
My other favourites on your list are [name]Matilda[/name] and [name]Josephine[/name], I’d love something like [name]Josephine[/name] [name]Matilda[/name] nn [name]Josie[/name] or [name]Matilda[/name] [name]Josephine[/name] nn [name]Tillie[/name].
[name]Rose[/name] [name]Athena[/name] its stunning too, my [name]SIL[/name] has reserved [name]Athena[/name] incase she has a daughter lol, but I’m clouded a little by the fact [name]Rose[/name] is a top 100 name in the UK, I don’t think thats true in the US though so ignore me! And [name]Rosie[/name] is sweet.
[name]Violet[/name] and [name]Elsa[/name] are lovely too, I just don’t love them as much as your other options, but honestly if I met a little girl with any of the names on your list I’d be incredibly impressed 
So basically, my faves would be, in order, [name]Penelope[/name] [name]Jane[/name], [name]Clara[/name] [name]Primrose[/name], [name]Matilda[/name] [name]Josephine[/name] and [name]Rose[/name] [name]Athena[/name].
Best of luck with your decision 