DedWards

I just realised something. With Teferi's Puzzle Box out, Psychosis Crawler will die because there's a split second that you have no cards in hand, making Psychosis Crawler a 0/0. If I'm wrong about this, let me know.

How's that?

Sadly I don't. Mostly because I don't have some of the cards I want for it, so I'm unable to test it...

That is ultimately up to you. Personally, I'd run 4 to get maximum effect out of it. Just be prepared to never keep what is in hand...

Ask and ye shall receive :P

http://www.mtgvault.com/dedwards/decks/sprouting-tokens-pauper/

I've been using it in my Presence of Gond + Midnight Guard Pauper deck. In fact, I've geared my deck to run off Sprout Swarm with the Presence of Gond being an alternative, though 'infinite', option :p

Honestly, I've never played Commander, so I wouldn't know what would be missed the least.

I'm collecting a bunch of Phoenix to make a Phoenix trial deck too. In mine, I'm wanting to run Braid of Fire for 'free' mana to pay for their return effects (the ones that require them).

I've seen an interesting build using these creatures that must be sac'd and Ooze Garden... Thinking about it now, Mimic Vat would be awesome too.

Rhys is legendary and Nissa is a planeswalker. Due to legend and 'walker rules, you can only have 1 out at a time, making any extra copies in hand 'dead card's. I'd reduce these to 3x at most.

Seeker of Skybreak and Wellwisher are preventing this deck from beginning Modern legal. Essence Warden does similar to Wellwisher and Umbral Mantle can untap the equipped creature.

Other cards you may want to consider:
Heritage Druid - lots more mana. You can tap creatures with summoning sickness to its ability.
Ezuri, Renegade Leader / Joraga Warcaller - more use for the excessive mana.
Gilt-leaf Ambush - instant speed 2 1/1 elves with a chance of temporary deathtouch. Also as a Scry type effect.
Druids' Deliverance - sideboard card. Fog with Populate on it.
Sundering Growth - sideboard card. Naturalise with Populate on it.

Personally I'm not that fond of Coat of Arms. I prefer Door of Destinies, but in an elf deck, Ezuri, Renegade Leader and Joraga Warcaller do a better job, imo.

A graveyard return card that might interest you is Unburial Rites. It has flashback, so it can be used twice :p

Killing Wave is cool, but I've come to like Mutilate more. While both get around indestructible and regeneration, Mutilate has a slightly higher chance of guaranteeing the kill as the opponent can pick an keep a few key creatures off Killing Wave (I've done this a few times off an opponent's KW and won).

I run a mono black Heartless Summoning based deck that I think might give you a few ideas:
http://www.mtgvault.com/dedwards/decks/heartless-black-modern-2/

I'd love to help you streamline this deck, but the biggest problem I'm seeing is that there's too many combos, leaving little space to streamline. If you could lower the number of combos, I could help with the streamlining.

Sprout Swarm? Can be a steady supply of Saprolings to use the Thallids' abilities.

Swarm Yard? It regen's insects and spiders. And I just checked Gatherer, you Commander is an Insect Wizard, so Swarm Yard can help keep her on the field

FYI, Teferi's Puzzle Box does stack. A friend has a similar deck and we looked up the rulings. Each Puzzle Box will trigger and resolve separately, allowing for more cards drawn in 1 turn, making Cerebral Vortex one hell of a kill spell.

Had an idea this morning and had to share it. I figured out a way to do this on turn 1 with 5 cards (7 if evasion is necessary), but sadly one of the cards is on the Modern banned list (Blazing Shoal)

Chancellor of the Forge - drops the 1/1 with haste
Swamp
Blazing Shoal - discard the Chancellor to give +7/+0 (8/1)
Mutagenic Growth - pay 2 life for +2/+2 (10/3)
Tainted Strike - +1/+0 and infect (11/3 infect)

And if evasion is necessary:
Simian Spirit Guide - Discard for {R}
Apostle's Blessing - use the mana from Spirit Guide and pay 2 life to give protection from whatever is in the way.

I own a set of Earth Surge, that's why I thought of it :P

I agree that it can be daunting to look for stuff on Gatherer, but that's why the filters (all those drop down menus) are so awesome. What I find annoying though is having to use American spelling to find what I'm looking for. I've often had to retype the key word(s) because of this...

Earth Surge?

Wild Nacatl? It was unbanned in Modern.