This is a very interesting topic. The natural place to start is of course the Old Testament itself. First, we have to clear some things up. "Yahweh" or "Yahu" and "El" were two distinct gods in the Caananite pantheon. This is actually reflected in the Hebrew text itself; if you read the early books of the Pentateuch, especially Genesis and Exodus, you will frequently find repetitions of passages, only slightly different. The most obvious example is the first two verses of Genesis; read them side-by-side, make a list of the order in which God creates things, and try to reconcile them. It's not possible, except with some extremely contrived arguments.

Now another thing is obvious even in translation - in Gensis 1 and the first three verses of Genesis 2, God is consistently referred to as "God". If you read Genesis 2:4 and onward, however, you will instead find the epithet "the LORD God". When "LORD" is written with capital letters, that means the Hebrew text says "YHWH". This name was considered so holy by the ancient Hebrews that one read "Adonai", meaning "Lord" or "Master", in its place. This was indicated by marking the vowels of "adonai" around YHWH, whence we get the mistranslation "Jehovah". Anyway, this practice was reflected in translation - we get Kyrios in Greek, Dominus in Latin, and LORD in English, all with similar meanings.

Why does this matter? Well, in many of the places where we have two apparently conflicting narratives, we find that one of the narratives frequently uses "YHWH" in one way or another, whereas the other sticks to "El" (translated God) or "Elohim" (translated God, but it's the plural form of God with the rest of the clause in singular, which is a way of emphasizing his importance or exaltation). Indeed in Exodus 6:2 - 3 we are told "I revealed myself to Abraham, to Isaac, and to Jacob as El Shaddai [usually translated God Almighty], but was not known to them by my name, Yahweh." The verses predominantly using "Yahweh" and "Elohim" respectively are conventionally thought to be part of two ancient literary or oral traditions, that of the Yahwist (J) and the Elohimist (E), dating back to approximately the 800's BC. The other two predominant traditions are "P" ("Priestly source"), sometimes thought to be the editor or compiler of the first two sources, typically dated to around 500 BC; and D (Deuteronomist), a separate tradition and the author of Deuteronomy and some of the later books, dated to around 600 BC. The dates are all quite rough and much debate surrounds them. Collectively, this is known as the Documentary Hypothesis, and it explains many features of the Bible.

As you see, the history of the Hebrew Bible is not very straightforward, and it consists of many different traditions that would later be unified. As for polytheistic origins, the link you provide brings up one of the best examples, Psalm 82:1, which can be roughly translated as "The most exalted El has taken his place in the divine assembly, he judges among the gods." Here "Elohim" is used both to refer to "God", and gods in plural. Many attempts have been made to translate this psalm to sound more in line with orthodox Christian thought, and often "gods" is placed within quotation marks or translated as "angels", but the Hebrew is really quite unambiguous. God is exalted above other gods, a king or judge of sorts, but he is one of several gods. Other examples, more or less obvious, exist. There is for example one passage where the Israelites flee because of a sacrifice made to Molech, but for some reason I can't find it at the moment...

Hints as to the identity of Yahweh can be found throughout the Bible. Isaiah 27 describes an apocalyptic scenario in Yahweh will slay Leviathan. Psalm 74:14 says that "It was you who crushed the heads of Leviathan and gave it as food to the creatures of the desert". These parellel the slaying of the sea monster Lotan, servant of the sea god Yammu, by a storm god Ba'al in the Ugaritic texts of Canaanite mythology. If we look at Job 38, it begins "And Yahweh answered Job out of the whirlwind." In Exodus 14:21, Yahweh parts the red sea by summoning a strong wind from the east. These are just off the top of my head - but they illustrate the likelihood that Yahweh was originally a storm god of some sort.

El, unlike Yahweh, appears in other Canaanite pantheons, and the word El, as indicated above, is also used to mean "God" (e.g., "Yahweh El"). In the Ugaritic texts El had a consort called Asherah, was symbolized by a bull, and was the supreme deity and father of other gods, and in the early 2nd century AD, the Greek writer Philo of Byblos identified him with the Greek titan Cronus. Indeed, up until the mid-6th century BC idols of Asherah appear to have been common in Israel.

What happened then, in the 6th century BC? Well, at the start of the century, Israel lost a war with Babylon, resulting in the destruction of Jerusalem, and the capture of many Israelites. This period is known as the Exile or Babylonian Captivity. During or after this period, the Israelites appear to have turned to exclusive worship of Yahweh, as the one and only god, as later writings are more clearly monotheistic.

The Babylonian exile was ended when the Persian king Cyrus (Kourosh) the Great conquered Babylon in 539 BC - we can confirm this date precisely thanks to an inscribed cylinder found in Babylon. Now, the Persians very likely (although it is in fact not known with full certainty) practiced Zoroastrianism, practiced in Iran up until the Islamic conquests in the 7th century. It is still practiced today, mainly by the Parsi, a minority of Iranian heritage in western India. Zoroastrianism was founded by Zoroaster (or Zartosht in modern Persian, actually Zarathustra in the original Avestan), likely around 1000-1100 BC based on linguistic analysis, give or take a few hundred years. Zoroaster was a reformer of Iranian religion, and preached worship of the Wise Lord or "Ahura Mazda", the one, unitary creator deity and the personification of all things good and moral. Other features that might sound somewhat familiar are angelic beings created by Ahura Mazda known as "Benevolent Spirits" (Spenta Mainyu), personifying virtues, and Angra Mainyu, the "destructive spirit" personifying all evil (and indeed, a controversy in Zoroastrianism has been whether Ahura Mazda directly created Angra Mainyu or not.)

In the latter parts of the book of Isaiah (Verse 40 onwards) we find an after-the-fact prophecy of Cyrus' conquest of Babylon, and praise of him as the "anointed one" or "Messiah", who delivered Israel from Babylon. Cyrus forged a covenant with Israel (in the name of Yahweh), incorporating it into his empire but tolerating local culture and religion. Indeed, here we also find the first explicit statement of monotheism, in Isaiah 44:6: "This is what the Lord says—Israel’s King and Redeemer, the Lord Almighty: I am the first and I am the last; apart from me there is no God." (translation from NIV). These become common later on, in texts also signified and easily dated by the use of Persian loanwords, and Yahweh is portrayed increasingly as the God most of us imagine today.

To sum it up: The God of the older parts in the Bible is an amalgam of the gods Yahweh and El. During a period of great hardship in the 6th century BC, the Israelites seem to have abandoned idolatry and turned to exclusive worship of Yahweh as the God of Israel. Following influence from Persian religion, Yahweh morphed into an increasingly exalted, universal, exclusive personification of Good. Later editors of the Hebrew Bible probably tried to scrub this fact from the older traditions, but they were not entirely successful. (EDIT: Of course, the practice of not pronouncing Yahweh was a consequence of his exaltation. Vowel marks were only introduced after the transitioining to monotheism.)

I hope this gives some insight. This is of course a vast topic with many angles - linguistic, archaeological, anthropological and literary, and opinions on the exact causes and influences that caused the transition are not uniform. However, the general idea of transitioning from polytheism to henotheism (worship of one deity in a pantheon) to monotheism around the period of the Exile, is not in serious dispute.