Have you thought of Witchbane Orb as a replacement to Leyline of Sanctity?

Witchbane Orb comes in too late. The reason why Leyline of Sanctity works is because it can protect your opener from decks like 8-Rack. By turn 4 the damage is already done.

If the leyline is only useful in your opening hand, then why not still run it in the side board? In your experience, when you've boarded in the leyline, were there times when it wouldn't have been a dead draw outside the starting hand?

Against 8-Rack there was one game where I drew Leyline on turn 4 with my hand empty and it bought me the time to get back into the game. The problem with Witchbane Orb though is that if I have it in my start hand it is vulnerable to such cards as Thoughtseize where Leyline is not. Besides that, given that the deck now runs green instead of white, Leyline can be removed for abrupt decay, which is not only a highly flexible removal card, but is also a stronger card than Leyline in most match-ups due to its flexibility. Thus, Leyline is removed more because there are better cards to run now that I have access to green mana, than because Leyline itself was somehow made worse by the fact that I no longer splash white.

Considering replacements for Hurkyl's Recall given that this deck simply plays a bit differently than the minefield and is nowhere near as reliant on its artifacts.
Considering Liliana, Heretical Healer  ^Flip as a replacement for Aggro match-ups given that when she is flipped she can pull Pili-Pala out of the yard as well. In creature form her lifelink makes her a very effective blocker as well.
Also considering Jace, Vryn's Prodigy  ^Flip as he can pull transmute spells/removal from the yard and re-use it. This makes him function as a form of pseudo-fetch, and he doubles as a blocker in creature form.
Other suggestions are welcome.

That's a really intelligent and original combo deck. Jace would be definitively a good inclusion here, even if he won't make the card transmute itself again (because you can't discard a card that isn't in your hand). However, his creature ability is pretty useful to you, he might distract the opponent from the combo you're trying to achieve and he gets back some Decays or other Pulses. ;)

A single Summoner's Pact might be interesting in terms of fetching since all of your combo parts are creatures. But not more than a single one since it won't fetch your win-conditions (zenith+command) and if your opponent has what it takes to make the combo fizzle you may die from it. :)

Here, take this upvote!

Summoner's Pact would be a great option if only I ran green creatures :P. Thank you for pointing out that I cannot transmute the spells which Jace, Vryn's Prodigy  ^Flip pulls out of the yard. I actually completely missed this fact. This makes him considerably worse in my opinion, as his only real use at this point is to pull cantrips out of the yard for card advantage (which, don't get me wrong, is EXTREMELY powerful), and pulling removal out for a second use...
This all said, I will probably still choose Jace over Liliana, as jace is far easier to flip, and most burn / aggro decks will simply zap lili before she flips anyway (and her inclusion would be as a counter to those decks, so this is a massive drawback). She also does not grant haste to the pili if she reanimates him, so her only true use is to act as a CONDITIONAL extra copy of grand architect.

Conclusively: Gonna make the jace change, and while i appreciate the suggestion for Summoner's Pact, it simply will not work in this deck.

How in the world did I forget the "green creature" part... Excuse me for this useless suggestion x)

Haha, no worries. I have made far worse. Just read The Minefield's update section. It's a bit embarrassing.

I really like the idea, awesome quick mana combo. Not a fan of Autumn's Veil if you need something to stop a counter spell Dispel stops the same blue/black spells you would normally want to stop with Autumn's Veil but has the added benefit of working on spells of any color so you can also avoid annoyances like Path to Exile or Lightning Bolt

Very valid point... And considering the value of Dispel vs Remand, I think I'll just stick with the Remands

Personally I'd be looking for a 1 drop counter for protecting your combo. The issue with a Remand vs a 1 drop is how easy it is for your opponent to instantly recast and still ruin your day and saving mana to protect yourself with a 2 drop slows you down 1 turn longer than a 1 drop. Spell Pierce and Swan Song could also work just fine, but that's all down to player preference.

Mana wise, once this deck goes infinite, the cost won't matter. Cavern of Souls (while not guaranteed to be present) should still help in this kind of situation. I will test it out... But I think that Remands greater versatility will be a greater boon than is cost is as a loss.

The more I test this deck with Remand... The more I keep wishing I had Dispel. Thank you for the suggestion steveoowns, I will be making that change.

I am thinking about adding Grisly Salvage to the deck. I have updated the "Maybeboard discussions" section of the description, where I explain my reasoning for this change, and which cards I would drop to add the salvage. Any and all feedback on this change is much appreciated. Thanks in advance guys.

I have made the Grisly Salvage changes. If anyone thinks this is unwise, I am more than open to community feedback assuming you logically defend your position.

Alchemist's Refuge might make a great addition to the deck? Especially against control. The ability to bait a counterspell at the end of their turn for a grand arc or pala. Then either way if they take the bait and counter, you can postmortem lunge on your turn with impunity. As for the Grisly Salvage, I like them but would replace one with an ancient stirrings, it allows you another dimension in your play options, as it could tutor the top 5 for a land, pili-pala, staff, some of your SB stuff, but most importantly; it can drop a Grand Arc in your yard. Often players focus too much on hand size, the battlefield, etc when playing. It is quite easy to forget the card sitting innocuously in your yard. As a bonus to this, since grand arc doesn't need haste with his ability to start using it, that allows either postmortem lunge or profane command to just instantly win.

I am slightly confused by the Ancient Stirrings suggestion. It puts cards on the bottom of your deck, not into the yard, which is why I am running Grisly Salvage instead. Perhaps I am missing something?
The Alchemist's Refuge isn't a bad idea at all. At the very least it lets me go off during the declare blockers phase with nothing but a Pili-Pala on board. Or on my opponents turn when they tap out. Any suggestions as to what I might drop for it though? I am loathe to drop any mana fixing, as this deck wants to be able to hit
T1: U
T2: GB
T3: 1UU
I don't want to drop any more Cavern of Souls, and I can't afford to drop any basics... Maybe an Overgrown Tomb?

Oops I completely spaced it on the stirrings ability. I wouldn't replace a land with the refuge, you more than likely won't be using it for mana much (hopefully not). Maybe maelstrom pulse? I know it would be a hard cut but there are 2 in SB, and it's not always as relevant unless it's against tokens or twin, (Some other matchups too) but more often than not it's basically an abrupt decay for 1 more. Also, your curve is quite low, but not so extremely that I think running 21 land would hurt.

I think what I will do is either cut one pulse or one Dispel in the sideboard, given that Alchemist's Refuge will be most useful against decks which run a higher degree of removal/counter magic.

Yeah against control it gives you a great out, and it's less expensive than vedalken orrery... Although it does require more mana all at once with the refuge. You seem like a pretty solid deckbuilder, would you mind taking a look at my 5 color control? It needs more wincons, all my matches last FNM went to rounds, and one drew because I could control the board well, but not dig into a game finisher fast enough. Would appreciate it.

You might want to try playtesting Snapcaster Mage over Jace, Vryn's Prodigy  ^Flip. Jace seems a bit on the slow side to me.

While Jace, Vryn's Prodigy  ^Flip is a bit slower than mr. Snappy... The main advantage of Snapcaster Mage is that he comes with a 2/1 body. This makes him a decent blocker and puts the opponent on a faster beat down clock.
The drawback is that you HAVE to cast the spell which is given flashback on the same turn that you play Snapcaster Mage. With jace, you can wait to use his -3 until an opportune time. And until then, his +1 can slow down opponent creatures. To compound this, jace can re-cast more than 1 spell, which is extremely beneficial in a deck which can only run so much removal and so many cantrips.
Given that this deck does not beat down its opponent (ever) the drawbacks of Snapcaster Mage make him a slightly worse option than jace. If allies and zoo become decks as popular as affinity is, I may just make that switch. As is, I feel the meta still has enough control and combo decks as to make that switch... Ill advised.
Still a fantastic suggestion. Thank you electromancer

I havn't even looked at the list yet O read the description and comments and I can already see Snap is better. If you have infinite Mana and a jave you have to wait untill next turn to flip him and win, thus opening your combo up to removal. But if you have infinite mana with a win-con in grave you can play Snapcaster Mage and flash back for the win THAT TURN through removal.