Learn Hardcore Indonesian: Saya menaruh buku di rak atas.

Menaruh = to put/place (general, everyday).
Meletakkan = to place/lay down (a bit more careful/formal; common in writing).
Menempatkan = to position/assign a place (more formal/intentional, also used for abstract placement like staff). All three can work with physical objects, but for natural, spoken Indonesian about putting a book on a shelf, menaruh or meletakkan is most common; menempatkan sounds more formal/technical. Examples:
Saya menaruh/meletakkan buku di rak atas. (natural)
Saya menempatkan buku di rak atas. (grammatical but formal-sounding)

Why is it di and not ke before the location?

Use:

di for location (where something is/ends up): final location.
ke for movement/direction (to/towards). Because the verb already encodes the action of putting, the location is expressed with di: menaruh … di …. Saying menaruh buku ke rak atas is unnatural in standard Indonesian. If you want a clear “into” sense, use a different verb: memasukkan buku ke (dalam) rak.

What exactly does rak atas mean? Is it “top shelf” or “upper shelf”?

Rak atas means the upper shelf (as opposed to a lower one). If there are only two levels, this is the top one.
If there are many shelves and you mean the very topmost, say rak paling atas or rak teratas to avoid ambiguity.

What’s the difference between di rak atas and di atas rak?

Di rak atas = on the upper/top shelf (one of the shelves).
Di atas rak = on top of the shelf (on the upper surface of the shelving unit), or above the shelf. This is not necessarily on a shelf level. For “on the top shelf,” prefer di rak atas or di rak paling atas.

How do I say “the book,” “a book,” or “my book” here?

“the book” (specific/known): buku itu (or bukunya if context makes it clear).
“a book/one book”: sebuah buku or satu buku. (sebuah is a general classifier.)
“my book”: buku saya (neutral/formal) or bukuku (more intimate/literary).

Is buku singular or plural? How can I make it plural?

Bare buku is number-neutral (could be “book” or “books” from context). To mark plural:

Reduplication: buku-buku (books, general).
Quantifiers: beberapa buku (several books), banyak buku (many books).
Numeral: dua buku, tiga buku, etc. (No article needed.)

Can I drop Saya? What happens if I say Taruh buku di rak atas?

Dropping saya in a statement can sound like a fragment. In conversation, people often switch to the bare verb as an imperative: Taruh buku di rak atas. = “Put the book on the top shelf.”
For an informal statement, many speakers say Saya taruh buku di rak atas. (using the base verb taruh).
You can also topicalize: Buku itu saya taruh di rak atas.

Can I use the base verb taruh instead of menaruh?

Yes. In informal speech, taruh is very common: Saya taruh buku di rak atas. With the 1st-person clitic you may see kutaruh: Buku itu kutaruh di rak atas. The meN- form (menaruh) is a bit more formal/neutral narrative style.

Where does the location phrase normally go? Can I say Saya menaruh di rak atas buku?

Canonical order is: Subject–Verb–Object–Location: Saya menaruh buku di rak atas.
You can front the location for emphasis: Di rak atas, saya menaruh buku.
Saya menaruh di rak atas buku is ungrammatical; the object should precede the location PP.

How do I make a passive version?

Two common passives:

di- passive (formal/neutral): Buku (itu) ditaruh di rak atas (oleh saya). The agent with oleh is often omitted.
“Short” passive with a pronoun agent (very common in speech): Buku (itu) saya taruh di rak atas. Here the verb is the base form (taruh), and saya follows the fronted object.

Is the spacing of di correct? When is di written together or separately?

As a preposition meaning “at/in/on,” di is written separately: di rak, di rumah, di atas.
As a passive prefix di-, it is attached to the verb: ditaruh, ditutup. So your sentence has both patterns in different roles: di rak (preposition) vs ditaruh (if you used the passive).

How do I indicate tense/aspect (past, ongoing, future) with this sentence?

Indonesian doesn’t conjugate for tense. Add time/aspect words:

Past/completed: Saya sudah menaruh buku di rak atas.; Tadi saya menaruh…; Barusan saya menaruh…
Ongoing: Saya sedang menaruh buku di rak atas.
Future/intended: Saya akan menaruh…; Nanti saya menaruh…; Mau menaruh… (colloquial intention).

Pronunciation tips for this sentence?

r in rak and menaruh is tapped/trilled.
u in buku/menaruh is like “oo” in “book,” but a bit tenser.
Final k in rak is unreleased; final h in taruh/menaruh is lightly audible in careful speech (often very soft).
Stress is typically on the penultimate syllable: sa-YA me-NA-ruh BU-ku di RAK A-tas.

Any difference between menaruh and menyimpan?

Menaruh: to put/place something somewhere (single act).
Menyimpan: to keep/store (implies keeping it there for a while/safekeeping). If you mean “I stored the book on the top shelf,” use menyimpan: Saya menyimpan buku di rak atas.

Is rak the same as a bookshelf? What’s rak buku?

Rak = shelf/rack.
Rak buku = bookshelf (a shelf or shelving unit for books).
A closed cabinet is lemari; lemari buku is a book cabinet (often with doors).

How to be more specific: “the topmost shelf” vs “the upper shelves”?

“the topmost shelf”: rak paling atas or rak teratas.
“the upper shelves” (plural): rak-rak atas or rak bagian atas. To be definite, add itu: rak paling atas itu.