Iām so sorry about the loss of your grandma. 
I saw that you said you donāt like popular/common names, and I guess Iām confused because a lot of the names on your list are very popular. In case this is still an issue for you, Iāll list each nameās popularity ranking next to it. 
[name]Charlotte[/name]: (#87) I really love this name, and Iām wondering how you feel about combining [name]Charlotte[/name]'s sound with [name]Sonia[/name]'s S, to reach [name]Scarlett[/name].
Some more names you may like along the lines of [name]Charlotte[/name]:
[name]Scarlett[/name]
[name]Violet[/name]
[name]Annabelle[/name]
[name]Beatrice[/name]/[name]Beatrix[/name]
[name]Celia[/name]
[name]Clementine[/name]
[name]Caroline[/name]
[name]Cora[/name]/[name]Cordelia[/name]
[name]Claudia[/name]
[name]Diana[/name]
[name]Eliza[/name]
[name]Emmeline[/name]
[name]Eleanor[/name]
[name]Genevieve[/name] (nn [name]Evie[/name])
[name]Helena[/name]
[name]Julia[/name]
[name]Louisa[/name]
[name]Lydia[/name]
[name]Miranda[/name]
[name]Phoebe[/name]
[name]Rosalie[/name]
[name]Susannah[/name]
[name]Simone[/name]
[name]Vivienne[/name]
[name]Olivia[/name]: (#6)
Some less popular alternatives:
[name]Ophelia[/name]
[name]Lavinia[/name]
[name]Livia[/name]
[name]Amelia[/name]
[name]Celia[/name]
[name]Dahlia[/name]
[name]Georgia[/name]
[name]Juliana[/name]
[name]Lydia[/name]
[name]Vivian[/name]/[name]Vivienne[/name]
[name]Veronica[/name]
[name]Victoria[/name] (popular, though)
With most of these names, I really love [name]Scarlett[/name] in the middle. 
[name]Kate[/name]: (#139): I love this name, but think Iād go with the longer [name]Katherine[/name] with your last name. That said, [name]Katherine[/name] is #45 at the moment.
[name]Audrey[/name]: I love this name, too, but this is now #44.
[name]Audrey[/name] [name]Simone[/name]
[name]Audrey[/name] [name]Susannah[/name]
[name]Claire[/name]: #62 at the moment. Have you considered [name]Clara[/name]?
[name]Bella[/name]: [name]Isabella[/name] is the #2 name in the country, and [name]Bella[/name] is 122.
Some more [name]Belle[/name] names:
[name]Annabelle[/name] [name]Scarlett[/name]/[name]Simone[/name]
[name]Mirabelle[/name] [name]Scarlett[/name]/[name]Simone[/name]
[name]Bella[/name] [name]Simone[/name]
[name]Bella[/name] [name]Scarlett[/name] (although this may be too much Southern [name]Belle[/name]) 
[name]Avery[/name]: [name]Avery[/name] has become really trendy, and is now # 38 for girls.
[name]Julianne[/name]: At #693, I think this may be the least common name on your list. I think itās lovely, and I also love [name]Julia[/name] (popular) and [name]Juliet[/name] (much less popular), as well as [name]Juliana[/name].
[name]Juliana[/name] [name]Simone[/name]
[name]Juliana[/name] [name]Scarlett[/name]
[name]Amelia[/name]: I love this, too, but itās really popular now, at #68.
[name]Amelia[/name] [name]Scarlett[/name]
[name]Finleigh[/name] (though my hubby will never go for it!): Like [name]Avery[/name], this is becoming trendy now, too. [name]Finley[/name] is only in the 600s now, but I can see it becoming the next [name]Avery[/name]. What about [name]Fiona[/name]?
Some S names:
[name]Stella[/name]
[name]Susannah[/name]
[name]Scarlett[/name]
[name]Sasha[/name]
[name]Sally[/name]
[name]Sadie[/name]/[name]Sarah[/name]
[name]Jack/name: #32
Less popular ideas:
[name]Anderson[/name]
[name]Harrison[/name]
[name]Jefferson[/name]
[name]Lawson[/name]
[name]Samson[/name]
[name]Wilson[/name]
(I think the son names may be a possible way of honoring [name]Sonia[/name], too.) 
[name]Connor[/name]: #57
Less popular ideas:
[name]Beckett[/name]
[name]Callum[/name]
[name]Declan[/name]
[name]Donovan[/name]
[name]Finnian[/name]
[name]Kellan[/name]
[name]Quinlan[/name]
[name]Rowan[/name]
[name]Sullivan[/name]
[name]James[/name]: I really love this, but itās #17
Less popular ideas:
[name]Charles[/name]
[name]Edward[/name]
[name]George[/name]
[name]Henry[/name]
[name]Jude[/name]
[name]Leo[/name]
[name]Oliver[/name]
[name]Peter[/name]
[name]Simon[/name]
[name]Theodore[/name]
[name]Finley[/name]: In the 800s for boys, but gaining popularity amongst girls.
[name]Finnian[/name]
[name]Griffin[/name] (nn [name]Finn[/name])
[name]Noah[/name]: Very popular, at #15
[name]Gideon[/name]
[name]Judah[/name]
[name]Jonah[/name]
[name]Micah[/name]
[name]Samson[/name]
[name]Tobias[/name]
S names for a baby boy:
[name]Sebastian[/name]
[name]Simon[/name]
[name]Sullivan[/name]
[name]Samuel[/name] (popular)
[name]Samson[/name]
[name]Stellan[/name]
Best wishes to you! 