I think there are 669 full-sized cards in the deluxe set, of which 560 can be face down in your deck or discard pile.
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Apparently I double-counted the 80 cards from the starters, adding them to the deck-capable numbers without taking them from the original ānon-codexā count (because I was also trying to find a way to store an entire set in my briefcase). Iāll have more spares than expected.
Anyway, itās actually 672 full-sized cards in the Deluxe set (560 for face-down deck-capable), according to the rulebook (which matches my print+play sets). The BGG post is using numbers from the KS campaign page, which later added 2 more maps (for 12 total) and a 6th mercenary token (which was presumably added to make the 5-player game work).
Iām using Fantasy Flight Standard Clear for my PnP. Iāve used them for a few years and have been happy. They are fully clear on both sides with no holographic markers.
Iām testing this informally. With some of my extra Codex sleeves, Iāve sleeved 20 of my Yomi foil aces and put them on my desk at work. This is so I can shuffle/fidget with the cards while working/thinking. If I notice any wear issues, I can report back.
To me, the pebbled texture on the back of the KMC Hyper Mat sleeves makes them the only choice for games that require card shuffling. I used them for Yomi and I have no regrets. I sleeved Codex in them the night before last, they fit fine in the binders.
Useful thread! I wish I had sleeved my cards. When my brother in law was over to play with the core set, he goes, āYou oughta sleeve thoseā and I go, āWhy? Itās not like Iām gonna resell the cards for hundreds of dollars. Itās a board game. If it wears out, Iāll buy another copy.ā Yeah . . . shoulda listened. By now my starter cards have taken much more wear than my tech cards, and itās so easy to tell them apart when shuffling, that I have to close my eyes or use dice when drawing to really trust that Iām being fair.
So now Iām all [Newbie CCG player]āWhat are these sleeves you speak of?ā[/newbie] 
The tougher question to me is what do you guys use for binders? The ones that came with the core set are perfect in a whole bunch of ways that seem hard to replicate ā theyāre thin, have opaque double sided pages, and have nice wide slots that can easily hold multiple cards and are easy to get cards in and out of during active play. I have yet to match that elsewhere.
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I got my deluxe set with the official Codex sleeves the other day. I was a little disappointed by the sleeves. They arenāt super high quality, and some of them were inconsistently cut as well. The cards fit nicely into most of the sleeves, but some of them were too narrow, and a few of them from one box were not tall enough and the cards stuck out. Out of my 700 sleeves, I had to throw away around 30. Iād recommend getting KMCs or Dragon Shields instead.
They do look nice though.
I went to a generic office supply store and bought duotangs. Basically flimsy paper binders of different colours that have little bendy metal clasps that you can use to put loose pre-punched paper in. Then bought a bunch of loose card protector pages and voila. It doesnāt look anywhere near as good as the official binders, but it gets the job done.
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Out of my 800 Codex sleeves, Iāve had to throw away about 30 for the same reasons as you.
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Iāve noticed that among the official sleeves, there are definitely some āshortā ones where the card sticks out the top. Of the remainder of the sleeves, the card usually goes right to the top of the sleeve.
I need to remind myself to buy some clear sleeves for all the non-deck cards (heroes, workers, tokens). I donāt want to put them in the same sleeves, lest I accidentally shuffle them into a deck.
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I donāt know anything about sleeves, but I bought the KMC Perfect Fit sleeves in anticipation of getting my Deluxe Set.They were actually too snug on the cards and were causing them to bow, so I just ended up sleeving them with some crap ass Ultra Pro penny sleeves that are definitely anything but a perfect fit. I usually keep those on hands to throw together PnPs and prototype cards.
Not sure if Iām going to upgrade the sleevesā¦
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I just modified my setup a bit, and I now think itās awesome and perfect. All my starter decks and spec decks are in Codex sleeves. All my tokens, workers, heroes, and map cards (i.e. any card that never goes into your deck) are in clear Dragon Shield sleeves. 
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Same except Iām using white matte backs that were a decent price for the non deck cards. Donāt get to see the beautiful backs of the heroes and tokens but thatās okay 
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So far, Iām loving the feeling of shuffling with Codex sleeves. So smooth!
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KMC Hyper Matte Clear is the answer. Look great, feel perfect, just do it guys.
If youāre going to a tournament and thereās marked card concern, pick the color of your choice, just keep it Hyper Matte.
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My cards are sleeved with KMC Perfect Fits. Most cards fit fine, though my green and purple decks were cut a fractional millimeter wider, causing the bowing issue you mentioned. I was able to fix the issue by compressing the bowed-out cards for several days, causing the sleeves to stretch slightly, and the bowing to cease. This was done by shoving the sleeved Codex cards in a M:tG card box, then cramming M:tG cards into the box on either side of the Codex deck until I could fit no more cards in.
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For folders, I got some of these:
I wanted plastic so they would not get bent and torn like paper.
Sleeves - These are the only sleeves Iāve really ever used. They are REALLY consistent in terms of size and I can see card backs.
I think these were the pages:
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As Pointy Finger noted, KMC Hyper Matte is the way to go. https://www.amazon.com/gp/product/B01AQG34TQ/ref=oh_aui_detailpage_o01_s00?ie=UTF8&psc=1
The key point here is that these cards have a āpebbledā surface on the back of the card. This greatly reduces friction, making them noticeably easier to shuffle, and less likely to stick to one another. I think this is great for all games that require shuffling, but is doubly useful in Codex, because it means that the back copy of each 2-card duo is less likely to stick to the page when you remove it from the Codex.
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Hmm, Iām thinking Iāll probably spring for some sleeves for Codex, and get enough to put my Yomi cards in too. So the question is are the KMC Hyper Mat sleeves really 50% better than Dragon Shields to justify the cost?
(Amazon UK prices: KMC Ā£6/80, Dragon Shield Ā£5.50/100. I think Iāll need about 1000 to do the ~700 Codex ones and have enough for my half-dozen Yomi decks, so itās Ā£55 for 1k Dragon Shields or Ā£78 for 1040 KMC ones.)
How do you like the pages? After some BCW side-loaders were too tight (for 2x sleeved cards, anyway) and stuck out past the edges of the 3-prong folders, I hunted for some very hard to find Ultra Pro 18-pocket toploaders, and theyāre too tight.
Also, the folders Iād recommend are these Comix ones I found on Amazon (here), mostly because theyāre just like every other polypropylene 3-prong pocket folder, but they were $10 with Amazon Prime free shipping, and came in a pack of six in a very familiar set of colors (black, blue, green, red, purple, and white). I couldnāt find a bunch of matching binders for all the colors anywhere else anyway, so that seemed like an eerily perfect option. Finding just a different color for neutral if desired should be comparatively easy.
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