Some 10 plagues ideas I had...
Biblical Equivalent - Aetherlight Equivalent:
Plague of water into blood = Plague of water into oil
My thinking here is that you can't drink oil, neither could you drink blood.
Plague of frogs = Plague of rats (or mice)
My train of thought is that frogs and rats in multitudes are equally annoying, they can both get everywhere and into everything (rats can chew through iron, and mice can fit into anything they can get their head through), and when the plague is over, they die in piles that stink to high heaven.
Plague of gnats = Plague of snakes (or beetles)
Again, it's mostly an annoying plague, but you could die if enough gnats bit you, so beetles or snakes could fit this role equally as well.
Plague of flies = Plague of scorpions (or hornets)
Now it gets dangerous, with flies carrying disease and biting you in swarms. Scorpions could sting you in multitudes if there's enough of them, and even if you had an antidote, you'd be in excruciating pain, almost like a million bug bites. (Hornets could fit as well, perhaps slightly better in this particular scenario, as they both fly and sting/bite, but I thought it would be a good theme to put all three Snowmoorian Automaton types into the list of plagues.)
Plague of cattle death = Plague of Automaton rust
Cattle are crucial for food and are generally large, and Automatons are crucial for protection and are generally large. Rust would be very much like death for Automatons, as they would simply cease working, and collapse and crumble with the slightest breeze.
Plague of boils = Plague of clothing fog rot
This plague seems to attack the vanity of the Egyptians, so fog rot in fog rot-proofed clothing seem sufficient to attack the vanity of the Academy inhabitants.
Plague of hail = Plague of avalanches
Chunks of ice as large as your fist? I couldn't think of anything to replace this except avalanches, but it fits.
Plague of locusts = Plague of baby crocodiles
Now, you may think "Awww, bebe cwocodiwes! Gimme a huwg!", but remember, these are carnivorous animals, attacking any food sources they can get, and they'd eat you alive if they could. Bring a certain desert insect to mind?
Plague of darkness = Plague of a blizzard
Darkness so thick you can feel it is something so unique, that a blizzard is the only thing that fits in its place (except for a massive flood, but I thought that was a bit overkill).
Plague of death of firstborn = Plague of mental illness of firstborn
This was the toughest plague to replace, but after many headaches, I found a sufficient explanation. Egypt was severely crippled from the other plagues, and the final plague destroyed any hope of rebuilding their dynasty for many, many years.
What could be so devastating to Baron Fairrow that it would result in him sending the remainder of his students away (I'm making the assumption that the students who came to the Academy against their will are the Israelites), never to be seen again?
If the finest and brightest of his pupils suddenly became as dumb as a box of rocks, with the IQ of a one year old, Baron Fairrow would see all hope of presenting the Emperor with a train-full of fine Autofficers crumple, and with it, all reservations towards letting whoever Martin Ambrose demands go with him, leave.