I cannot say yet how much Puzzle will hurt the deck since i have not been playing a lot lately. Not being able to reuse Scramble Switch is a thing and sometimes being able to pull an energy from the discard pile can make the difference but it is not something totally breaking the deck by any means. It hurts much more Zoroark-Gx than this deck to loose puzzles.
If you want to play 4 copies of Ninja Boy it is up to you but since you also have VS Seekers 3 is fine. 3 Ninja Boy with 3 VS Seeker i think should be a minimum since the deck relies on Ninja Boy that much.
Regarding Skyfield while you are right that you absolutely need to keeping the pokemon you need for the matchup in your deck, sometimes you need to dig into your deck on the first turn and this means you sometimes need to bench your Pokemon to do that. This is when Sky Field can sometimes come in handy. It also helps thin the deck and enables you to get rid of those pokemon that will not be useful for the matchup. Basically you will not want to bench the pokemons you need but only those you don't. If the pokemon you need ends up into your hand do not bench it, use Pokemon Communication (this is a very good reason to play Pokemon Communication because you need to make sure you do not end up with the pokemon you need in your hand when you want to Ninja Boy into it because this can screw your game). Remember also that Sky Field should only be temporary. It's main purpose is to help you dig in your deck on the first few turns or when you really need to but it is something that ideally you do not want to use. If you use it, the best thing to do is to bench as much as you can and hope to clear your bench afterwards with Field Blower. Having benched basic pokemon (especially Unown) will help you clear your easy prizes and will help you avoid loosing from a Guzma or Lysandre. Remember that this deck's main win condition is stall and you cannot achieve this if your opponent can play around it. So basically, you want to quickly clear your bench after using a Sky Field and benching a lot so that you do not end up having more prizes on the bench that the total of prizes remaining for your opponent.
Also, there are many stadiums you could use instead of Sky Field, this is just one archetype. In this version i am playing Colress with Sky Field but you could also try other options that are just as good. Sometimes I shake things up and play Parallel City or Fairy Garden also. This deck by playing so many pokemons will also most of the time make you benefit from your opponents stadiums as well. Most notably Rough Seas, Altar of the Moone and Brooklet Hill but this is dependent of what pokemon you are using with the deck.
Here is what i would consider staple for the deck to be consistent, the rest is up to you to decide depending on what you want to beat. Note that i suggest playing a minimum of 8 energies.
* 2 Shaymin-EX ROS 77
* 1 Jolteon-EX GEN 28
* 2 Tapu Lele-GX GRI 60
* 2 Unown AOR 30
* 1 Glaceon-EX FCO 20
##Trainer Cards - 30
* 2 Mallow GRI 127
* 1 Rescue Stretcher GRI 130
* 1 Pal Pad UPR 132
* 3 Ninja Boy STS 103
* 4 Ultra Ball FCO 113
* 2 Guzma BUS 115
* 3 VS Seeker ROS 110
* 2 Pokémon Communication BLW 99
##Energy - 10
* 2 Rainbow Energy SUM 137
* 2 Prism Energy NXD 93
* 4 Double Colorless Energy XY 130
Finally, i highly recommend playing Machamp-Ex and/or Tauros-Gx to counter 2HKO decks and Pheromosa-Gx just to have the donk option (works very well against Greninja, Buzzwole and Nightmarch). Also, Comfey and Magearna seem like optional but are very useful in some matchups (Gardevoir-Gx, Sylveon-Gx, Lapras-Gx, Darkrai-Gx, Hypnolaser/Seismitoad/Seviper and many more). I included Diancie-Ex just recently because it hits Rayquaza-Gx for weakness and comboed with Tauros or Machamp can help against Zoroark-Gx since Dark pokemon will deal 50 less damage on Diancie-Ex because of her resistance and her ability combined. So after Diancie tanks the first Zoroark hit, you can Ninja Boy and take it out. But i have not experimented enough with Diancie-Ex in the last patch so i cannot tell if she will make the next cut. Latias-Ex finds its use against Trevenant Break, Xurkitree-Gx and things like Hoopa, Ninetales and Aegislash-Ex but it is up to you to decide if it is an inclusion you want to keep or not.