For the most part I'm still using the same standard Endymion/Mythical Beast combos, however I increased Cerberus from 1 to 2, since it is a free way to get Jackal King/Garuda in my hand, and he's also a nice target for Magicians' Souls going second so that I decrease my chances of drawing into him and bricking (sometimes, when I already have a scale that I can't readily pop), and also for Selene to bring back so I can banish one of my opponents monsters.
I used to have 2 of Purple Poison and 1 Black Fang Magician, as well as 1 Allure of Darkness for those darks, but they were just really bad to have if I wanted to combo off and go into a full board of negates, as I would usually want to save my normal summon for Blue Boy for the spellbook engine, and also it just seemed really dumb to pendulum summon them out to link into crowley if I didn't already have Jackal King/Mighty Master in hand, as I would just use the spellbook engine to draw into my negate cards then with no way to summon them out.
Instead, I put in 2 of Magician's Restage and 1 Foolish Burial. This has turned out to be a pretty solid way to rack up spell counters while also adding more monsters to my field for link materials and drawing more cards. Here are some examples (its entirely possible this is just common knowledge for Endymion players but I am also fairly new to playing Yugioh):
1: If I had practically no pendulum monsters/search cards in hand, but I had 1 Restage and Foolish Burial, I would use foolish burial to send a Magicians' Souls to the GY, then Restage to bring it back and then use Souls to pop Restage/ (sometimes Institution too depending on my spell counters) to then draw more cards. This is really my main use for Foolish Burial, but I will also sometimes use it to send Reflection or Cerberus to the GY as a target for Selene, depending on whether I go first or second, if I don't have Magicians' Souls in hand to do this. If I do have one of my starters, then again this is also a really good way for me to rack up a ton of counters to search/special summon.
2: If my starting hand had Spellbook of Knowledge and no blue boy or secrets, but I had either Magicians' Souls or Jester Confit--preferably Souls--as well as a Restage (or if I draw into Restage with Knowledge instead of like Servant/Reflection/Abductor/Spell power mastery to start my combo) then I would use restage to bring back it back (and then send less helpful spells to the GY to draw more if its Souls).
3: If I have Souls and Restage in hand, then I activate souls, then Link 1 into Artemis, then Restage to bring back Souls, pop Restage to Draw 1, and then Link 2 into Crowley to run my spellbook engine.
There's probably more combos, but these are just the main ones I tend to use. Again, with all of these examples, assuming the worst: I am unable to scale anything and therefore I am not racking up counters, but with all my draws I will almost always get a starter and enough spells to get its counters, but if I am to scale even just one thing, then I can just get counters for days.
Also, Restage is generally just a good target for my Mighty Master to destroy whenever I want to pop him from my high scale on turn 1. I normally target Citadel if I have it out, so that I can use Citadel's effect to avoid destruction, but then Mighty Master won't get his counter for additional protection (occasionally I will also target Mythical Institution if I feel like I don't need it).
For my extra deck, I replaced Abyss Dweller with Bagooska since Bagooska seems like a more general way to negate monster effects (although I did side Dweller for me to switch out with Bagooska depending on the match up).
I replaced Geonator Transverser with Apollousa. Transverser was really just in there as a potential out to Dragoon, but I almost never used it to do that. In fact, I pretty consistently have been able to out Dragoon with Accesscode, so it made more sense to free up a space for Apollousa to get more potential negates, although I usually will end my turn with Selene out and Reflection in my hand/the GY so that I can bounce back a potentially bad extra deck summon/normal summon (and then I'll also keep an extra space for me to use Garuda to bounce back another similar summon if I can't use it to MST a facedown or an annoying continuous spell/trap. I still need to find a way to work Apollousa into my combos without removing my other negates.
Lastly I took out Thousand-Eyes Restrict, since Millennium-Eyes just felt like a better target for my Instant Fusion to its ability to chain onto a monsters effect and grab it for myself (especially the ones that "Can't be destroyed by card effects"), and I replaced it with Day-Breaker, for its ability to pop spells/traps, free up my scales, and also to get some more counters for my negates to use. I toyed around with using Saryuja instead to fix bad hands, but usually, by the time I have enough cards out to use his draw 4 effect, I would have already played most of my hand, so I would be removing 4 monsters from my field to draw one card, this being after I had already pendulum summoned/normal summoned.
When I'm siding out, I will usually take out 1 Cerberus, 1 Jester Confit, and 1 Restage. If I need to side out more than 3, I will then side out 1 Blue Boy and 1 Secrets, and I normally don't side out more than 5 cards, but also I might just not know how to side deck (please keep in mind that I have just been playing for a little more than a month at this point). Of course, it goes without saying that I'm interested in hearing any differing opinions you guys might have regarding side deck decisions or card ratios, since I am also posting this in part to get some feedback to improve my deckbuilding. Thanks!