Congratulations! :)
Love Rupert & Arthur.
Emmett is too 'American-sounding' for my own tastes and what would it be shortened to? Em, perhaps? Your other choices are distinctly masculine so you might want to rethink this one if a clearly male name is important to you.
I like Alfred and Albert but not the nicknames you have suggested. The shine off these two names has also gone for me, as I feel they peaked in the 2000s. Of the two, I prefer Albert. I feel it would be difficult to get people to call your Alfred 'Freddie' when Alfie is the more prevalent and, in many ways, more intuitive nickname.
I can imagine all of your choices on a little baby, boy or man so, while they aren't all ones I'd go for myself, I think your boy will be fine with whichever one you pick!
As for your girls' names, I don't like either Lorelai or Rory. Aren't they the names from the Gilmore Girls, in any case? I would assume a little girl named Rory was named Aurora. Not one for me.
I like Elizabeth but not Betty (I prefer Bessie, Lizzie, Libby); Maggie but not Margaret; and love Alice.
All in all, very sensible lists and I am sure you'll come up with one you and your DH like from them!