I am also working on a Kruphix deck. Helix Pinnacle and Seedborn Muse look like a good idea for him!

You're going to need more land than you've left room for, I consider a good amount to be about 35 lands in EDH.

Engulfing Slagwurm + Lure is something pretty cute that you could do

if you have any artifacts that you feel you absolutely need, Fabricate wouldn't be a bad addition. As well as, Akroma's Memorial perhaps

Discoduck, I was not aware of Seedborn Muse I will definitely find a place for it.

Dethjakal major yes on Lure that'd be hilarious to put on Slagwurm.

Part of what I am looking for is tips on what to remove out of this to make room for the mana base I need.

If you like Lure then try out Vortex Elemental for some more funzies. Even without Lure, Kruphix allows for plenty of mana for forcing creatures to block.

Teferi, Mage of Zhalfir , Leyline of Anticipation and Vedalken Orrery can all find a place here.

Sylvan Library , Greater Good , Momentous Fall for drawing/filtering. Mana dorks: Sylvan Caryatid , Lotus Cobra , Birds of Paradise .

I think I would run Opportunity over Flow of Ideas since this isn't monoblue and instant speed is relevant.

Thank you all for your suggestions. I've spent the last few days trying to wittle this down. I've now gotten it down to have room for the Mana base and added a core mana base.

Any tips on improving things is still greatly appreciated.

Tbh i think you're missing one of the main upsides of kruphix's mana ability; being able to play artifacts and eldrazi for super low amounts of mana relatively early. Think about it, he enables you to play cards like Blightsteel Colossus or Kozilek, Butcher of Truth after maybe one or two turns of him out on the battlefield. That is extremely debilitating and can be considered as a bit of a dick mvd but its still a very powerful idea if you're willing to be the target of other people for awhile. I like the deck though, and a +1 from me.

Have you thought of Master Biomancer and Cyclonic Rift ? Both of those are extremely valuable - mainly rift - in EDH, you also have a whole array of blue negation which is pretty free if you have massive amounts of floating mana with Kruphix. Try out Pact of Negation or Summoner's Pact maybe even Blue Sun's Zenith to get any and every card in your deck ever? You can also run Jace, Architect of Thought as a form of draw power. You also kinda have the infinite amount of cards printed as blue draw power. Also surprised Snapcaster Mage hasn't been considered.

Blue Sun's Zenith is even more powerful in a deck with kruphix as your commander since you dont have to discard cards after you play it. That and the infinimana that you can sometimes produce. Also the praetors, ESPECIALLY Jin-Gitaxias, Core Augur , are good staples of edh and even more valuable in this deck. Gitaxias can make your hand massive and you dont have to worrycabout discarding so you could pretty much either take over the game completely from that point onward, or deck yourself lol.

Personally, Triumph of the Hordes over Overwhelming Stampede

Divination over Opportunity perhaps, lower the curve a bit

Sorry for so many comments, Spell Crumple is great with Tunnel Vision . So is Reito Lantern and Junktroller

Sorry for not responding everyone. Thank you for your responses,

@8BitNecromance I already have Blue Suns Zenith in the deck, and definitely will be considering Jin Gitaxias.

@Zephros I personally don't think Master Biomancer quite fits this deck. Cyclonic rift is definitely one to consider, I will have to see if I need the last minute protection like that. Snapcaster mage is definitely a good card and will figure out if it fits in my deck.

@dethjakal I ended up cutting Overwhelming Stampede and Tunnel Vision from the deck. I think I prefer the extra cards drawn over the 2 mana less cost but thank you for the suggestion.

Peregrine Drake and Deadeye Navigator , they interact well with Tooth and Nail and your mana theme. You need more mana dumps (X cost cards, possibly artifacts that mill or something).