The armour values of toughness powers don't need to stack with this power at all (just apply the powers in the proper order: armour then swarm), but I see little reason not to allow the expanded stress track to apply.

Ah, sorry; what I meant was that the Armour from Toughness wouldn't apply if you got your attack past Swarm Body's Catch. Armour is already useless if this power applies to an attack, but I'm considering making it useless (or less powerful) even if this power doesn't apply to an attack (i.e. no bugs with Armour 2 against area attacks).

And I like the penalty-based wording on Amorphous better than the original. It just needs a little bit of adjustment in case someone is grappling you without Might.

Reworded.

But I'm still not convinced about the balance of Swarm Body. It might be roughly balanced against ordinary attacks, but it's clearly superior to Toughness against very large attacks. And for those who play above Submerged, that might mean all attacks.

Yeah, but... the thing about very large attacks is that they're quite often, well, very large. It's simple enough to describe any evocation as being large enough to zap something that's non-Hulking Size, and even on those swarms large enough to be of Hulking Size, it's two extra shifts to blast the whole zone and render this power moot. Mortals should have a fairly simple time negating it, given the all the Fate points they get (and how well-versed they need to be in Maneuvers; in fact, screw the evocation attack, the wizard should be trapping the target in a Ring Of Fire to keep them condensed enough for a strike).

(For context, I am currently GMing an 18 refresh game. One of my 5 PCs would be pretty well shut down offensively by this power, and two would have semi-serious trouble with it. Supernatural Toughness would be easier for them to deal with by a fair bit.)

What is the first PC, and what are the second two?

As a defensive power, this is cool, but its Catch is really, really broad. I don't see how they can be exploiting many other non-weapon-based (i.e. Cold Iron, Holy, Fire) Catches if they can't deal with this one.

That said, I am giving serious consideration to downgrading or outright invalidating any Inhuman-Mythic Toughness taken alongside this power. Tessa's tough in Mantis-form, but her bugs (shapeshifting to a form that includes this power) can just be stomped on.

Hive Mind would seem to interact problematically with the Cashing Out clause of Cloning Blues, causing you to suffer a consequence but denying you the normal resulting FP.

Further, I am hesitant of that clause in its own right, as exemplified by a hypothetical area attack hitting yourself and your clone at the same time then taking you out far more easily than it otherwise would.  And god forbid you have more than one clone with you.
(just think of what would happen if you had 3 clones with you and get hit by an area attack that would force you and them to each take a mere mild consequence: either you're taken out the next time you get hit, or you're losing clones)
I'd recommend instead giving each clone a default of only one mild consequence (+ those from high skills) of its own, and having upgrades grant more consequences, but then not have those consequences count against those available to you.

Sorry, the Hive Mind thing was written in a rather confusing fashion, so I don't think we're working on the same page. I've reworded it now. How does that look?

Ah, thanks! Fixed.

Thoughts on the power itself?

MULTIPLE BODIES [–7]
Description: Two heads are better than one, and many hands make light work; you can split off a single copy of yourself, which shares your memories and abilities. Depending on the upgrades taken, this power could represent the fission of an ooze demon, the splitting up of a swarm of lesser creatures, or even the magical duplicative hair of Sun Wukong.
Skills Affected: Physical skills.   
Effects:
Cloning Blues. You may produce a single, exact copy of yourself as a supplemental action. This copy is indistinguishable physically, though mystical observation shows it to be a construct of ectoplasm. The copy has the same skills, stunts and powers as you, and has your memories at the time of creation; the only mechanical difference (besides the normal vulnerabilities of ectoplasmic constructs) is that their High Concept is “Copy of a [Original High Concept]”. You have no special ability to communicate with your copy (outside of invoking their High Concept to guess what they’ll do next), and do not learn what they learn unless you recall them (requiring a free action while in physical contact), at which point they dissolve into ectoplasm and you gain all their memories since they were created. You and your copy have separate stress tracks; however, your supply of consequences remains the same, and must be split between the two of you. You do not cash out (see page 206) for consequences suffered by your copy. If your copy is killed (rather than being recalled) you may not generate a new one until the next scene (if you are killed, your copy immediately dissolves into ectoplasm). Note that despite having the same powers as you, your copy does not acquire their own item slots from spellcraft powers, and cannot create its own copies through this power.

We Are Many [-1]. This upgrade increases the number of copies that you can have active at the same time by one. You may take this upgrade multiple times, increasing the number of potential copies by one for each purchase. Note that, should one of your copies be killed, it does not completely remove your ability to create new ones until the next scene; it simply reduces the maximum number you can create this scene by one.

Von Neumann’s Magic [-2]. The We Are Many upgrade is a prerequisite for this one. Your copies can create copies of their own using this power. They use the creating copy’s memories, rather than your own, but are otherwise created just as described in Cloning Blues. They are still your copies, and therefore cannot exceed the number of copies you may have active at once.

Distant Recall [-1]. This upgrade allows you to recall your copy from a distance as a free action, instantly dissolving it into the ectoplasm from which it was formed. If you have a Hive Mind (below), this upgrade becomes free.

Hive Mind [-2]. You and your copy share minds. You know everything they know, and vice-versa, allowing real-time sharing of information and memories without the need for recall. This has numerous applications, and adds two shifts to any maneuver made by you or your copy to co-ordinate an action with the other (see page 208). However, with this upgrade, you and your copy share the same mental stress track; this means that you are treated as the same target for the purposes of psychic attacks, allowing them to damage both of you at once. In addition, you and your copy both suffer from the taggable aspect produced by taking a mental consequence, regardless of which of you actually “spent” the consequence in question. Other appropriate temporary aspects might also "spill over" in this way.

Ontological Inertia [-0]. This upgrade cannot be taken by characters with positive refresh. Upon taking this upgrade, your copies become just as “real” as you are (arguably, not very), making the question of who the original is rather moot. As a result, rather than imploding into ectoplasm upon your death, your copies will remain intact (and may produce another copy to replace you, if they have that ability). This will sometimes result in one of your copies acquiring true independence, at which point it becomes a separate character with the ability to create its own roster of copies; a number of creatures native to the Nevernever reproduce in this manner.

Split Skills [+4]. Rather than being able to produce exact duplicates of yourself, you must split your power amongst the bodies you produce, resulting in a set of weaker copies. Whenever you produce a copy, all of its skills default to Mediocre (+0). You must provide it with skills by reducing your own and adding an equivalent number of skill points to its sheet (see page 65). For example, by reducing a Superb (+5) skills to Good (+3), you would acquire two skill points to raise one of your copy’s skills to Fair (+2). Skill points taken from one skill need not be spent on that same skill; it is acceptable to reduce your Might in order to increase your copy’s Lore. Your copy may not have any skill ratings higher than your original score in that skill. Keep a record of your character’s original skill ratings; they return to their previous level once the copy is recalled (if the copy is killed, it is treated as being recalled one scene later).
   
Split Power [+Varies]. This upgrade provides you with refresh equal to half the total refresh cost of your supernatural powers (excluding Multiple Bodies, but including any refresh spent on We Are Many), rounded down. Whenever you produce a copy, you must total up the cost of your supernatural powers (excluding Multiple Bodies) and divide it by two. This is the new refresh cost of the powers you and your copy may possess. You must first spend this refresh on powers that are core to your High Concept (i.e. (i.e. Living Dead for a Zombie or Lawbreaker for a Warlock), and you cannot produce a copy without such powers. Often, this will result in a simple reduction of power; splitting Supernatural Toughness into two iterations of Inhuman Toughness, or reducing Evocation and Refinement into two iterations of Channelling. You cannot provide your copy with supernatural powers you do not possess any version of. If you have any spare refresh, you may temporarily assign it to appropriate powers for you or your copy.

Keep a record of your character’s original powers; they return to normal once the copy is recall (if the copy is killed, it is treated as being recalled one scene later). If you can produce more than one copy, then you must divide the refresh cost of your supernatural powers evenly again between yourself and each copy, each time you produce one. It would probably be wise to produce a number of "templates" based on the kind of power-sets you could give different numbers of clones, to save time.

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Incidentally, the Shen work pretty well if you stat them out as a single Kong-sized version with Multiple Bodies, the Split Power and Ontological Inertia upgrade, and We Are Many x3. A Kong can then split off into a pair of Gorillas, a trio of baboons, or a quintet of Chimps, with its power being reduced appropriately with each split.

SHEN
High Concept: Demonic Poo-Flinging Kong
Skills
Fists: Good (+3) Might: Good (+3)
Most other physical skills are Fair, the rest are Mediocre.
Powers
Breath Weapon [–2] (incendiary poo)
Wings [–1]
Supernatural Strength [–4]
Supernatural Toughness [–4]
Inhuman Recovery [–2]
*The Catch [+2]: Only functions against mundane sources of damage.
Hulking Size [–2]
Multiple Bodies [-7]
*We Are Many (x3) [-3]
*Von Neumann's Magic [-2]
*Ontological Inertia [-0]
*Split Power [+8]
Stress
Mental oo, Physical ooooooooo, Social oo
Total Refresh Cost: –17

So, you get a +2 to your refresh is your Catch is something that anyone with an awareness of the supernatural would know about, and only +1 if it's something you could uncover with research. Except (and I'm looking at the pdf-version here, since my hard copy has yet to arrive, so things might have changed) the example for a Catch given under Physical Immunity states that a fire demon would get a +3 Catch on its Toughness, with a vulnerability to Cold. +2 because Cold is easy to come by, and +1 because research should uncover it.

Setting aside the fact that I'm having trouble thinking of how to easily assault someone with cold, shouldn't the fact that a fire demon is vulnerable to cold be blindingly obvious? Or at least, obvious to anyone who's ever played a game with elemental vulnerabilities (such people likely outnumber those who've read Bram Stoker at this point)? Does the Catch discount take common sense into account, or is that covered by assessments/declarations?

Same question for, say, a chlorofiend. Giant plant monster; the first reaction of any human being when considering weaknesses would be "fire"... so would it get that +2 for a widely-known weakness, or would I need to "research" it? Basically, is "this creature has a widely-known weakness" the same thing as "this creature's weakness is really obvious"?

My first attempt at making a homebrew power for this game; I needed it for a "worm that walks" style baddie, but it could also be used for mundane swarms of things (assuming you're dealing with a swarm as one creature rather than statting up each individual rat, anyway).
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SWARM BODY [–3]
Description: Rather than one entity, your body is made from a multitude of lesser creatures, making you more difficult to harm.
Musts: This power comes with its own specific Catch (see page 185). If you suffer physical consequences, they must take into account the non-singular nature of your body; a demon with a body made from five-hundred-and-two stone crabs is unlikely to suffer a Broken Arm.
Skills Affected: Endurance, other physical skills.   
Effects:
Chipping Away. Physical attacks cannot inflict more than one stress on you at a time; no matter how devastating the blow, it can only target a small part of your “body”. The effects of this power are applied after additions and subtractions from weapons and armour; wielding a sword will not appreciably increase one’s ability to fight off a swarm of bees (by the same token, bees do not classically benefit from wearing kevlar).

Specific Catch. Unlike other Toughness powers, Swarm Body comes with its own preset Catch, which offers no discount. The effects of this power are completely bypassed by area attacks; that is, those attacks that encompass a great majority of the target’s body. Diminutive insect swarms would be thus affected by sprayed insecticide, while a human-sized enemy would be vulnerable to flamethrowers or suitable evocations, and even larger swarms might require more extreme measures to seriously damage. Note that a clever maneuver might force a swarm into a confined space or formation, and thereby reduce the size of the attack necessary to harm it.