Your collection of questions conflate a few things: 1) what is だ・です in modern Japanese, and 2) how did だ・です derive historically.
Because of #2, #1 is a bit ... messy. :) So let's start with the history.
「です」は、「でございます」が変化したもの,
This isn't an explanation of what です is now, so much as an explanation of the historical derivation. Shogakukan's 国語大辞典 provides this description:
「でござります」→「でござんす」→「であんす」→「でえす」→「です」の経路で生じたものという
Meanwhile, the modern plain form だ derives as:
「にてあり」から出た「である」が、〔dea〕→〔da〕と変化したものという。→であ・じゃ・である
Modern で (which actually appears from around the 1300s-1500s) is understood to have evolved from earlier にて (which is still used in formal writing). Classical copular ("is") verb あり equates to modern verb ある.
Looking now at the particular parts of your post:
「で」は「だ」の連用形。 「で」is the conjunctive/continuative form of 「だ」
Well, yes, in the modern language. But historically, だ derives from で + ある -- so this is not a regular kind of conjugation paradigm.
To sum it up, 「です」 is a variation of 「だ」(its polite form).
Yes. Though I might not use the term "variation" so much as "polite form".
It is also a contraction of 「でございます」,
It derives from a contraction of でございます, but I don't believe it's considered to be such a contraction in modern regular usage.
which in turn is the same as 「であります」(forgetting here about the differences in usage)
It's not quite the same as であります. Note that ございます is the humble version of あります. That difference in usage is important. :)
that is formed by attaching 「で」 to the verb「あります」.
Yes -- but note also that であります is not a verb unto itself, but simply the particle で plus the verb あります.
So, after this long trip, we arrive to the conclusion that the "hidden verb" behind 「です」, is in fact ある, which is actually (or at least more close to) the sought after "to be".
Historically, yes. And if you dig around in classical Japanese and older stages of the language, you'll find just that -- あり serves as the primary copular verb.
In modern Japanese, however, だ・です is the primary copular verb: it closes a predicate, and (optionally) supplies social register information ("politeness"). One no longer says things like 綺麗にあり, one says instead 綺麗だ. Similarly, instead of 本にてあり, one says 本だ.
Related thread touching upon social register:
I hope the above covers the bases for you. If not, please comment and I can edit the post accordingly.
Addendum
I missed a question of yours that I'd meant to answer.
Can we really call です（or だ) an auxiliary verb?
Depends. :) "Auxiliary verb" (助動詞) is a kind of loose category in Japanese school grammars. The article on the Japanese Wiktionary provides a table showing the various things that get this label. Some of them I really don't agree with: そうだ and ようだ are listed here, and those are clearly そう or よう + copular だ・です -- and だ・です is right there in the table as it's own pair of rows at the bottom. Others like らしい, ない, and たい are adjectival in form and function. Many, like させる or たがる, have full conjugation paradigms (i.e. they have forms for all conjugation slots), whereas others like negative supposition まい or positive supposition う are defective (i.e. have incomplete conjugation paradigms; see Defective verb at Wikipedia).
Basically, it's a grab-bag of odds and ends that get stuck on the ends of other things (often, but not always, verbs). This category was also previously called simply 助け言葉 ("helping words"), and this vague moniker is a clue to the vagueness of the category itself.
So, "can we really call です（or だ) an auxiliary verb?" Sure. So long as we're clear on what we mean by "auxiliary verb". :)
