Jonah Sebastian - I like both of these names a lot, and together they make a very handsome combo.
Caleb Theodore - Absolutely love both names, love this combo.
Henry Leonard/William - I would opt for Henry William just because Henry and Leonard start out with the same sound, but it's not super obvious or horrible so Henry Leonard is okay too.
Isaac - This name has grown on me a lot since The Fault in Our Stars. From your honoring list I love any of them with it: Isaac Samuel is probably my favorite, then Isaac James, Isaac Oliver, and Isaac Robert. Non-honoring suggestions: Isaac Finley, Isaac Jude, Isaac Morgan, Isaac Thomas.
Boys' name suggestions (including the ones given as middles above): Finley, Jude, Morgan, Thomas, Alastair, Ezra, Finn, Lennox, Rory, Quinton/Quentin, Beckett, Owen, Ronan, Tate, Felix, Miles, Ethan, Eli/Elijah/Elias, Lucas/Luke, Gabriel, Daniel, Gavin, Holden, Elliot, Graham, Tobias, Stellan, Logan, Joshua
Vivian - I love Vivian, and for a while I debated on the spelling I like best and eventually landed on Vivienne. Vivian is my close second favorite though. I love from your honoring list Vivian Pearl, Vivian Margaret, and Vivian Mary. I've never heard of Samaire but it would go nicely with Vivian as well. Non-honoring suggestions: Vivian Louise, Vivian Kira, Vivian Ruby, Vivian Adele.
Eleanor Leigh - I love this combo, have always loved Eleanor with the nickname Ellie or even Nora. And my middle name is Lee so I like (and am used to) how it sounds as a middle.
Hazel - Another one I really like. From your honoring list, I like Hazel Samantha, Hazel Margaret, and Hazel Pearl. Hazel Mary is nice but to me it kind of sounds like "Hail Mary" so I'm not sure. Non-honoring suggestions: Hazel Emmeline, Hazel Clara, Hazel Josephine, Hazel Seraphina.
Girls' name suggestions (Including the ones given as middles above): Louise/Louisa, Kira, Ruby, Adele, Emmeline, Clara, Josephine, Seraphina, Charlotte, Adriana, Evangeline, Lorelei, Rosaline, Emilia/Amelia, Miranda, Beatrice, Alice, Daisy, Piper, Ingrid, Mae/Maeve