Muktol

With [[Springleaf Drum]] this shouldn't be that much of a problem.

I would switch [[Iron Apprentice]] for [[Arcbound Mouser]]. Yes, you only can move the counters from Arcbound onto other artefact creatures, but this should be no problem in the deck, and lifelink is a really valuable ability.

[[Intangible Virtue]] then. And I would remove [[Daxos, Blessed by the Sun]] for something like [[Crusader of Odric]], [[Seraph of the Masses]], [[Silverwing Squadron]] as you have enough life-gain and these would profit more from a high number of tokens on the field.

Not a vampire, and again something with cmc3, but with all the deathtouch [[Hooded Blightfang]] could be worth a look.

Without informations on the deck, which weren't there when I wrote this, how should I know? Normally I get to see decks here that are finished or just need tuning.

Good red carddraw is a rare one. [[Wheel of Fortune]], [[Ogre-Head Helm]], [[Dangerous Wager]] or the other draw/ discard spells, like [[Magmatic Insight]], [[Tormenting Voice]], [[Cathartic Reunion]], and so on, come to my mind.

[[Rise of the Hobgoblins]] is illegal in this deck and you need to remove another 20 cards to get down to 99 + Krenko

[[Defile]] instead of [[Cut Down]] and [[Morsel Theft]] instad of [[Essence Extraction]]?

[[Dawnbringer Cleric]] could be used instead of [[Raptor Hatchling]] if you prefer versatility over power. [[Dreadhorde Arcanist]] (budget-question) in combination with [[Curse of Stalked Prey]] allows you to re-cast [[Pyroclasm]] each turn, which could also be interesting.
[[Gauntlets of Light]] or [[Solid Footing]] could give the deck some options.

Pauper uses [[Thorn of the Black Rose]]/ [[Phyrexian Rager]] as draw-creatures, and [[Read the Bones]]/ [[Sign in Blood]] as draw spells.
Personally I'm running [[Duress]] in the sideboard in case I have to many removal and too few targets for them.

What about [[Cast Down]] or [[Defile]] as removal?

Super scary to see (At least in commander) would be [[Goblin Sharpshooter]] with [[Basilisk Collar]]. Poisoned machine-gun anyone?
If you want to add first strike to the deck I would rather use [[Viridian Claw]] because it can be played and equipped faster. With low power creatures the trample is not really needed.
Depending on the meta/ legality [[Thorn of the Black Rose]] could also be an option.

What about [[Vraska, Swarm's Eminence]]?

A deck description is always a good thing to give for other players, especially when starting new with the game. You can put details on the strategy of the deck, about the budget you want it to be in, legality, if you're willing to buy/ trade cards, and other informations you want to share with us into it. This makes it a lot easier for other people on this website to help you, especially with decks that feature a lot of cards with only 1 or 2 copies, as it can be hard to guess what you want to achieve with such a deck.

[[Last Thoughts]] would be a cipher card that allows you to draw a card while [[Rogue's Gloves]] or [[Zephyr Boots]] could do the same in artifact form.

Some cards from newer expansions allow you to create ally tokens: [[Captain's Claws]], [[Gideon, Ally of Zendikar]], [[Retreat to Emeria]].
Shapeshifters could also be an interesting way of getting allies on the field: [[Irregular Cohort]], [[Mirror Entity]]

Sadly not a rogue otherwise [[Brineborn Cutthroat]] would be a good card. And to make the most out of [[Faerie Vandal]] you're lacking carddraw.

[[Light from Within]] and perhaps [[Springjack Shepherd]]

Basically this should work. But be aware that :
05.10.2018 If the target creature's power is no longer less than the attacking creature's power as the ability resolves, mentor doesn't add a +1/+1 counter.
So if you attack with a [[Aurelia, Exemplar of Justice]] and a [[Hopeful Initiate]] and put the Mentor ability on the stack first and Training above it, so that Training will trigger first, [[Hopeful Initiate]] will only get 1 +1/+1 counter because he has the same power as [[Aurelia, Exemplar of Justice]] when her ability checks for higher power.

Personally i would opt for [[Soaring Thought-Thief]] with [[Malevolent Hermit // Benevolent Geist]] as sideboard replacement. Tough I'm more a pauper player, so my opinion might not be worth that much ;)
[[Relic Golem]] or [[Vantress Gargoyle]] could also be worth a look.

Sadly [[Nephalia Drownyard]] isn't legal for pioneer any more, this would be a good addition. [[Codex Shredder]] would be a weaker option that would allow you to mill continuously. Library manipulation could be done using [[The Biblioplex]]

Personally I would (re)move 2 [[Hero's Downfall]] into the sideboard and add [[Cast Down]] instead, and switch when playing against decks with high legendary or planeswalker count.

Some suggestions without knowing the original deck or what you changed:
[[Gitaxian Probe]] is banned in pauper (https://magic.wizards.com/en/banned-restricted-list). [[Clairvoyance]], [[Peek]], [[Ingenious Thief]] or even [[Glasses of Urza]] could be an option to replace it.
[[Murder]] and [[Victim of Night]] could be replaced with [[Cast Down]], [[Evolving Wilds]] could be replaced with one of the new Streets of Capena search lands: [[Maestros Theater]] or [[Obscura Storefront]]