Ok, man, here's what I opted to add to the deck and why, along with what I suggest you cut.

1. Chaos Warp

To make room for this, we'll be cutting Dragonspark Reactor. As a removal spell, having to build up counters overtime and ultimately pay six mana to deal damage to one creature isn't a good rate at all.

Chaos Warp, on the other hand, costs half the mana, is an instant, and can remove any permanent type. This will be a big upgrade to your interaction.

2. Wurmcoil Engine

For Wurmcoil, we'll cut God-Pharaoh's Gift. I see why God-Pharaoh's Gift is in the deck, but at seven mana, it doesn't pull its own weight, and there are cheaper ways we can make token copies of things.

Wurmcoil Engine costs one fewer mana and is a nightmare for opponents to deal with efficiently, especially when Brudiclad can copy the tokens it leaves behind. In general, Wurmcoil will be more bang for your buck.

3. Big Score

Mnemonic Sphere either works out to be four mana, draw two cards or one mana, discard it, draw one card, and neither of those is a good rate. So, instead, we'll play Big Score.

Yes, it also costs four mana and makes you discard. However, you can discard whatever card you like, draw two cards, and make two treasure tokens. For the same price, we're getting the same amount of card draw plus some really nice ramp.

Casting this on turn four also means you can cast your commander next turn, so keep that in mind.

4. Academy Manufactor

Crystalline Giant isn't a bad card. But. Academy Manufactor is a fantastic card. Take the Big Score mentioned above as an example... If you cast it with Academy Manufactor in play, you get two treasures, two foods, and two clues.

It's simply too good not to be playing.

5. Thopter Spy Network

Golden Guardian // Gold-Forge Garrison is listed as ramp in your list, but it's far too slow to get you ahead in the early game when ramp matters most. Plus, the four cmc + the two to activate means this lands on turn six naturally.

This is a problem when you consider your commander is also six mana. Turn six, you don't want to choose between the Guardian and Brudiclad. In its place, we'll play the all-star Thopter Spy Network - It churns out flying artifact tokens and can be a serious card draw engine for the deck.

6. The Locust God

Here, we're removing Goro-Goro, Disiciple of Ryusei to play The Locust God. Goro-Goro doesn't do much for you. He's not on curve to give haste to anything crucial, and a five-mana 5/5 token only if you control an attacking modified creature isn't great.

The Locust God is everything you want for your build - He's a resilient threat in the air, creates tokens for Brudiclad, and can draw you cards, which fuels his own ability and creates tokens.

I know it costs more mana, but your original list was loaded at the two drop spot, so we'll be ok with this swap. 

7. Blasphemous Act

The next card we'll add is Blasphemous Act. It's a classic and one of the best red board wipes. Also, since you're going wide with tokens, you'll often be able to cast it for quite cheap.

We'll cut Kairi, the Swirling Sky to make room. Overall, it's a fine card, but it competes with Brudiclad on the curve and gives your opponents some control of things, considering it needs to die to trigger.

You won't be sorry to have a Blasphemous Act in its place.

8. Loyal Apprentice

There are decks where Lizard Blades belongs, but Brudiclad is not one of them. Simply put, it does nothing for our overall game plan. That said, we'll swap it for something that does.

And that's where Loyal Apprentice comes in. It's a reasonably aggressive card sometimes, and the token production works very well alongside Brudiclad... Big improvement here.

9. Curiosity Crafter

Merchant's Dockhand is terribly inefficient. It only appears to cost one mana, but to do anything, you've got to pay four more mana, and tap down several artifacts all for a single card. We can easily cut this card.

In its place, we'll play Curiosity Crafter. Overall, it's less mana, a flying 3/3, draws a card whenever you deal damage with a token (insane in this deck), and makes it so that you have no maximum hand size.

10. Mechanized Production

Myojin of Cryptic Dreams has to be cute here - Don't get me wrong, it's a nasty card with a significant effect, and making those three copies would be powerful. That said, it costs way too much mana.

Instead, we'll play Mechanized Production for half the cost. It allows you to copy whatever artifact it's enchanting at the start of every turn. Then, if you control eight or more artifacts with the same name as one another, you win the game!

You don't need anything fancy here—eight treasure tokens and the game is yours. We'll focus on this more in the higher-priced upgrades.

11. Thopter Assembly

Pentavus is pretty bad as a seven mana 5/5, that you can pay additional mana into to make a 1/1. On top of that, he shrinks himself while making that token. Eight mana + remove a counter from your creature for a 1/1 token = Not very good.

Thopter Assembly, on the other hand, is much better. Less mana, same power, and toughness, and any time you find yourself thopterless (which I'm sure you know happens all the time), you'll get a whole swarm of 1/1 flyers.

This is also amazing for rebuilding after a board wipe and will give you a lot of resilience.

12. Padeem, Consul of Innovation

I love Psychosis Crawler as a card, but in this particular deck, it serves no real purpose. In its place, we'll play the must-have Padeem, Consul of Innovation. Hexproof for all your artifacts and built-in card draw... What's not to like?

This will make your opponent's life very difficult. :) The flavor text and art are great. Massive, massive upgrade here and cheaper on mana.

13. Skullclamp

With as many 1/1 tokens as we're making, we have to play Skullclamp. For one mana, you equip this to a token, it dies to the -1 to its toughness, and you draw two cards. Once you're set up, you'll be drowning in card advantage, thanks to this.

To make a space, we'll cut Reinforced Ronin, which is a much worse rate.

14. Sai, Master Thopterist

Gift of Wrath pumps a creature up and creates a 2/2 token when it dies, but that's pretty underwhelming for four mana, especially when you consider that the +2/+2 and menace don't exactly move the overall game plan along. We can cut this with no problem.

In its place, we'll add Sai, Master Thopterist, which moves the deck along amazingly. We have 34 artifacts in the deck now, so he'll churn out the tokens. Plus, he has some lovely card draw tacked on if you need some cards. Lastly, as a 1/4, he's a pretty good blocker in my experience.

15. Solemn Simulacrum

Discover the Impossible isn't a terrible card if you build around it since you can sometimes cast spells for free. However, there are only four instants or sorceries in the deck with a mana value of two or less, and three of them are counterspells that you probably won't need to cast on the spot.

In short, in this build, the card reads three mana, dig five cards deep, and put one into your hand, which isn't very good.

In its place, we'll add Solemn Simulacrum. It's ramp and can block and draw you card. Plus, a four-man ramp is great for us because it puts us right on track to cast Brudiclad the following turn, assuming we make our land drop on turn five.

16. Counterspell

Disruption Protocol is basically Counterspell with an extra cost. So, we'll swap it out for Counterspell with nothing but an upside.

17. Unexpected Windfall

Reality Heist is powerful (especially when cast for cheap), but I'm not too fond of the idea of being able to whiff on hitting anything good. In other words, we want something more consistent in cost and reward.

Unexpected Windfall is that consistency. It's always gonna cost four mana and a card, and you'll always get two cards and two treasures. Again, this is card draw and ramp that sets you up perfectly to cast your commander the following turn, even if you've missed a land drop or two.

18. Third Path Iconoclast

Planar Incision isn't bad but there aren't enough things we want t fliker to include this in the deck. Sure, it could save something from removal but aside from that it feels like a dead card.

In its place I added Third Path Iconoclast which should pull some serious weight in the deck.

19. Saheeli, Sublime Artificer

Karn, Living Legacy is good on paper. His +1 could be helpful, but the powerstone entering tapped slows things down some, and we have plenty of cards that it won't be able to be used for.

The same is true for the -1; it works when it works. If it misses, you won't get much out of the deal. This card is an excellent example of a high ceiling (good at its best) and a low floor (bad at its worst) without much in-between.

My replacement card, Saheeli, Sublime Artificer, on the other hand, consistently does what you want it to—Make creature tokens and copy things into bigger things.

Lands

I didn't get fancy with the lands for the $50 upgrade. Many just cut a few lackluster lands that weren't needed, reducing the amount of basic land as it was pretty high. The big improvement here is the artifact lands:

These are essentially free artifacts for key cards like Thopter Spy Network that we don't want to miss out on playing. For the Citadel, we'll cut the Evolving Wilds and then cut one Island and one Mountain for the other two.

This leaves are color ratios unchanged and adds some synergy to the deck.

Shivan Reef

Shivan Reef is a great budget dual land that doesn't enter tapped. And considering the number of colorless cards we have, you won't even have to take one damage too often. For this, we just cut a basic island.

Buried Ruin

This card is phenomenal in the deck as more recursion for the most impactful artifacts. We'll ditch Rouge's Passage as its mainly for "go tall" strategies with bigger creatures.

Kher Keep

This just gives you a small (but sometimes game-changing) way to produce more creature tokens. Considering how much we've improved already, we can certainly afford to cut Surtland Frostpyre, which enters tapped and has a much worse ability for far more mana.

Temple of Epiphany

Last but not least, we'll remove one last basic island to play one Temple of Epiphany. This can smooth out your draws in the early game with no real downside. And in the late game, when you may not need more land, it still has some utility in setting up your top decks.