Simply love names!
I really like the name Maia. My favourite comboniation is Maia Isabelle followed by Maia Elise. However if you want to honour someone Maia Lotti is great choice. Maybe Maia Charlotte would work as well as a honour name for your grandma. Lotti is generally a nickname for Charlotte.
I love the name Claire that would be my pick.
You could even combine the names to Clarita. You would get both names on one then.
Some middle name ideas... Genevieve, Juliet, Isabelle, Vivienne, Rosalie, Margo, Irene, Therese, Marie, Madeleine, Marguerite, Simone, Louise, Giselle, Lucille, Gabrielle, Violet, Beatrice, Phoebe, Susannah.
I prefer the spelling Eveen. How about Eeveen?
I like Yael. It is more unexpected.
Congrats on your upcoming baby.
For names I like Abbey from your list. I myself would use the full Abigail with the nickname Abbey, there is also the spellings Abby and Abbie to consider. Madison is not my cup of tea but I love the nickname Maddie/Maddy. Same with Madison, Kendall is not for me, it reminds me to much of the boys name Kenneth and the nicknames Ken or Kenny. Gracyn reminds me of the boys name Grayson.
Some ideas for you... Mallory, Savannah, Cassidy, Avery, Riley, Aubrey, Macey, Jasmine, Ashley, Kayleigh, Aspen, Delaney, Eden, Lindsey, Emery, Rowan, Hadley, Lacey, Lauren, Teagan, Lilah, Molly, Ivy, Zoe, Lexie, Hannah, Sofie, Norah, Emelie, Chloe, Alexis, Phoebe, Alison, Carly, Stephanie, Natalie, Aaliyah, Hayley, Skylar, Joanne, Grace, Gracie, Lydie, Leah, Leslie, Morgan, Lorelei, Kenzie, Paige, Taylor, Maeve.
For middle names your taste seems to slide more to classic names. Some ideas... Sophie, Harriet, Emily/Emelie/Emilie, Madeleine, Madeline, Lucie, Isabel/Isabelle/Isobel, Rosalie, Rose, Hannah, Caroline, Amelie, Juliet/Juliette, Vivienne, Gabrielle, Lilian, Anneliese, Giselle, Annabel, Felicity, Audrey, Evangeline, Simone, Claire/Clare, Ann/Anne, Jane/Jayne, Naomi, Norah, Eleanor/Elinor, Grace, Elise, Elisabeth/Elizabeth, Celeste, Evelyn, Coralie, Ariel, Camille, Genevieve, Sarah, Violet, Iris, Adelaide.
My favourites from your list are Wren, Marlowe and Scarlett. I think those three all work well with a brother named Grayson. I prefer Addelyn spelt Adelyn and Millicent just seems to be a completely different style to Grayson.
For middle names I like Noelle and Rose. However all your options work well with the first name which it is paired with.
Some pairings I like with your names listed above are...
Some other names you may like to continue the colour theme... Amber, Beryl, Coral, Jade, Garnet, Opal, Pearl, Ruby, Violet. Have you thought about using Rose as a first name?
Some other names you may just like... Rowan, Harper, Madison, Jasmine, Kayleigh, Everly, Sloane, Caitlin, Shiloh, Cassidy, Robin/Robyn, Lorelei, Savannah, Grace, Aubrey, Skylar, Cadence, Blythe, Briar, Ashley, Emery, Taylor, Elle, Reese, Eloise, June, Belle, May, Florence, Marian, Adele, Rosemary, Bryony, Cleo, Esme, Elodie, Jessamine, Constance, Olive, Ione, Estelle, Elinor, Isobel, Tierney, Sybil, Avis, Clemetine, Harriet, Adair, Adelaide, Marguerite, Felicity, Faye, Inez, Lucy, Amity, Raine, Verity, Dorothy, Rosalie.
My vote goes to June Simone. To me it's sounds like your not sold on Simone as the first name. You still have your honour name in there but in the middle name spot. June could be nicknamed Juniper.
You have got some great opinions already.
Mary Margaret - Love the alliteration. A nickname could be Mary-Pearl as Margaret means pearl. However I do agree with previous poster's it does sound like a very Catholic combo to me.
Clara Grace - I love this name combo. Flows nicely.
Anna Claire - Flows nicely together.
Emma Jane - Emma is to over used for me. Jane is nice though.
Jane Anne - I think the two names are lovely but not together. I think it sounds choppy, just my opinion though.
Sarah Katherine - Love this one. Sarah Kate is a lovely nickname.
Knowing the sibling names my favourite would have to be Sarah Katherine nicknamed Sarah Kate.
Without knowing much else my personal preference is Lincoln. It goes well with John. Lincoln John is very handsome.