There are 9 zeppelin parts total, 3 of each kind, in or near various wyvern nests (one in a treehouse). At least one rudder, compass and crystal is required to get to Aleroth. Here is a map of the fjords (spoilers), showing the rough locations for the 9 parts. Alternately, from the walkthrough,
-Crystal 1: on the tiny island just south of the entrance to the fjords; climb
up the ladder and retrieve it from on top of Yggdrasil

-Crystal 2: on a low cliff east of Camp Sentinel View, across the water from
Camp David

-Crystal 3: on a cliff in the middle of the bend just before the entrance to
Rivertown Gorge [EDIT on the same ledge as a boarded-up cave door]

-Rudder 1: a short ways east of the Camp Freedom teleporter

-Rudder 2: halfway between the Imps' Lair and Camp David

-Rudder 3: on a low southwest cliff near the exit to Rivertown Gorge

-Compass 1: on the cliff directly opposite Rudder 1

-Compass 2: high up above Moor's shack, just northeast of the entrance to
Keara's Flying Fortress

-Compass 3: on a cliff just before the bend on the way to Rivertown Gorge


The gem for Kenneth is near the end of the channel south of the harbour, near a wrecked ship, but no longer in it.


There are a couple malachite gems that can be purchased, and if you reload at malachite veins (save before running your crosshairs over them) you can get up to 4 malachite gems out of each (1 or 2 are relatively easy to get, 3 are possible with a bit of patience or luck, while 4 are quite rare).
There are a couple malachite veins in the well cave in High Hall, in addition to the quest reward (near the end of the cave, off the path to the left, but they can only be found before triggering a cutscene).

From the walkthrough (malachite gem section):
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| Malachite Gems |
----------------

Needed for the best enchants in the game, these rare and elusive gems are
quite precious. While it's near impossible to get all of them in a single play
through of the game, using this list, you should be able to get enough to
comfortably enhance your favorite weapons, armor, and jewelry.

Broken Valley:
-You can buy two gems from Merchant Lamotte in the Broken Valley village.

-The only other gem you can acquire before adventuring in Orobas Fjords comes
from waking up the sleeping trio east of Lovis' tower.

Orobas Fjords:
-On the path leading to High Hall from the Depleted Ore Mine, you encounter a
traveling merchant by the name of Carleton. He sells a malachite gem, but be
careful! At the time of this writing, there is a bug that causes you to be
unable to buy from him if you open trade via dialogue. Click the Trade button
instead and you will be able to buy the gem.

-You receive two malachite gems as a reward for completing the quest 'The
Horror of High Hall'. If you read Beatrice's mind, the reward becomes four
gems, making this the single largest (reliable) source of malachite gems.

-If you read the goblin Charlie's mind while on the quest 'Reaping the Seeds',
a small treasure chest appears in the nest on top of Yggdrasil, and a
malachite gem is inside.

-If you chose Radcliff as your enchanter, you can trade the gem he asks for to
a pair of goblins in exchange for two malachite gems. Doing so will bar you
from ever getting a second upgrade for your workshop, but it's probably worth
the trade off unless you enchant a whole lot and hate utilizing your runners.

Malachite Veins:
The rest of the malachite gems can be found randomly in malachite veins. There
aren't many, and each one isn't guaranteed to have even one gem (though forum
rumors suggest up to four in a single vein). If you save your game before
approaching any given malachite vein, you can always reload until you get more
gems. However, it's probably not worth reloading as long as you get at least
one.

-The first malachite vein you're likely to encounter is in the Depleted Ore
Mine, just past the three pedestals with the red, blue, and dark books on top.
[ED: there are 2 veins here]

-There are two malachite veins near the Patriarch. The first is along the
eastern wall and is relatively easy to find. The second is hidden behind some
rocks on the western wall, very near an empty wagon sitting just in front of
the wooden platform you stand on when talking with the Patriarch.

-The last malachite vein is in the cave opened by the four treasure hunter's
seals. ...and those poor adventurers thought there was nothing of value in
there.

-According to Kein on the Larian forums, there is one more malachite vein in
the Well Cave at High Hall, but a thorough search of the entire cave has
turned up nothing. If you choose to search for it, it's supposedly in the same
room as Zagon and can only be claimed before turning into a dragon.