Why do we call an instruction book a "Manual"?

"Manual" is used for many things: "Manual Labour" - work done with the hands; "Organ Manual" - hands again; and I can see the link to the Latin "manu".

But why would a book of instructions be a "Manual"? Any ideas?

As you probably noticed, all those uses of "manual" you know mean "hands". Now try to link those two concepts - an instruction book and hands - what do you get? "Handbook", which is exactly what a manual is. Manual and handbook are synonyms, one coming in from English, the other from Latin languages.

As for the etymology itself, always consult Etymonline (emphasis mine):

manual (adj.) c.1400, from Latin manualis "of or belonging to the hand; that can be thrown by hand," from manus "hand, strength, power over; armed force; handwriting,"

So the shared root is probably from "handwriting" related to "hands", the same as "manuscript" comes from the original handwritten text.

Ultimately, yes, the noun manual derives from the Latin adjective manuālis, as was pointed out in Avner Shahar-Kashtan's answer. As it turns out, though, the history of the noun manual is different from that of the adjective manual, and reflects rather the original, Classical-era meaning of manuālis — in short, a book of instructions is called a manual not because it has handwriting in it, but rather because it is handy, if not actually hand-sized.

Now for the gory details. On the one hand, according to the OED, the adjective manual has the following etymology:

As adjective < Anglo-Norman manuel, manual, Old French manuel performed by hand, involving physical labour (c1200; in Middle French also ‘who works with his hands’) < classical Latin manuālis held in the hand, of a size to fill the hand (the sense ‘done by hand’ appears to be post-classical, as are ‘worked by hand’ and ‘who works with his hands’) < manus hand (see manus n.1) + -ālis -al suffix.

On the other hand, again according to the OED, the noun manual has the following etymology:

As noun < Anglo-Norman manuel, manual handle, handbook (compare Middle French manuel, 1539 in this sense) < classical Latin manuāle a wooden case for a book, a handbook, use as noun of neuter of manuālis. Compare Italian manuale (a1342 as adjective, 1673 as noun), Spanish manual (1377 as adjective, 1502 as noun), Portuguese manual (1548 as adjective, 1560 as noun).

Finally, according to Lewis and Short, we have that manuāle dates from the Classical period (with a citation from Martial, no less), a substantive form of the adjective manuālis at a time when it still had its original meaning of

of or belonging to the hand, for the hand, that is held in or fills the hand, hand-.

In particular, Lewis and Short suggests that manuāle, as a substantive noun, stands for something like inuolucrum manuāle, meaning "hand-size cover" (cf. "pocket(-sized) book").

As a comparison, the Croatian word for "manual" (the noun) is the calque (from Latin) priručnik, which very specifically translates as "something at hand/handy," and is lexically quite unrelated to, well, "manual labour."