I was actually quite amazed to discover, during the course of my own research, that IHVH has been identified with Set quite a bit. The Jews who lived in Egypt were considered disruptive due to their monotheism and their Shabbat (Sabbath) celebrations. The idea of having a "day of rest" every week was unheard of. Only royalty and nobility were normally allowed to enjoy such leisure; but here was a bunch of "little people" demanding to have a "weekly holiday" each week! And Hebrew monotheism was considered insulting to the Egyptian Gods. Normally in those days, if you went to live in a foreign land, you payed your dues to the Gods of that foreign land, so as to show respect for them on their turf. The refusal of the Hebrew leadership to do this was revolutionary at the time; it was even considered seditious. Hebrew monotheism and Shabbat observation were perceived as threats by the Egyptians, because they were thought to anger the Gods. And there was only one God they could think of who would side with "the little people," who would incite them to be "lazy" on a day ruled by a "malefic" planet (i.e., Saturday), and who would want them to be disrespectful toward the other Gods: i.e., Set. Egyptian disfavor toward the Hebrews was probably helped by the Hyksos invasions that occured during the 1600's BCE, since the Hyksos were Semitic, and Egyptian xenophobia is known to have intensified significantly after that event.
Later, writers like Plutarch and Manetho report stories in which Jews were outright accused of worshiping a donkey during horrific nocturnal rites, which were even reported to include cannibalism. The donkey, of course, was one of Set's sacred animals. In his Gods of the Egyptians, E. A. Wallis Budge quotes Plutarch's report of a story in which, after He was "cast out" from Egypt, Set-Typhon rode for seven days on the back of a donkey through a desert. When He found a place of safety, He "gave birth" to two sons named Judaeus and Hierosolymus - Judaeus being a Greek corruption of "Judea" and Hierosolymus being a similar corruption of "Jerusalem." It would appear that both Late Period Egyptians and Greeks both shared a common subversion ideology in which Jews were accused of secretly being criminally deviant Set worshipers, not unlike the "blood libel" myths that would later surface in such events as the Roman persecution of Christians, the European witch hysterias, and the 1980's "satanic ritual abuse" panic.
Another curiosity I find very interesting is when Don Webb reports in his Seven Faces of Darkness that certain names for the Jewish God were later adopted by first century Typhonians as names for Set. There are numerous spells in the Greco-Egyptian magical papyri in which Set-Typhon is identified as "IO" - which is both a Hellenization of "aai," the Egyptian for "donkey," and of "Iah," as in Yahweh - and "SABAOTH," which means "Lord of Hosts" in Hebrew. He even points out that the use of the name "IO-SETH," a combination of IO with the Greek equivalent of "Set," was specifically intended to resemble the Hebrew name "Joseph." Indeed, the tendency to adopt elements of Judaic mysticism into Set's cult seems to have been a common theme. We even see it in the twentieth century with Kenneth Grant, who identified his notion of "the Tunnels of Set" with the Tree of Qlippoth. We also see it with the Temple of Set, whose original founders were previously affiliated with LaVey's Church of Satan, in which rituals included recitation of the word "Shemhamforash" - the so-called "seventy-two-part Divided name of YHWH."
There is also the raging controversy among scholars of Gnosticism over the confusion of the Gnostic Seth (the third son of Adam and Eve, whose name is actually spelled "Sheth" in Hebrew) with the Greco-Egyptian Set-Typhon. For the most part there appears to be no major evidence for such a connection, but there does appear to be quite a bit of resemblance between Sethian Gnosticism and Typhonianism, especially in terms of their ascension rites. In any case, I am convinced that there IS a connection between Set and IHVH; in my own ritual experiences I've come to think of Set as the pagan "Truth" behind IHVH. It is helpful to remember that during biblical times, most of the Hebrews were actually polytheists, who were perfectly willing to worship other deities beside IHVH (such as the Goddess Asherah). Strict Hebrew monotheism was represented for the most part by the Hebrew priests, who were a minority. Much of the Old Testament consists of complaints made by this minority against the Hebrew majority and their "adultery" with other Gods. As for the identification of Set with Baal, this is a proven fact. The Hyksos themselves are probably the best reference for this, and Lewis Spence reports in his Ancient Egyptian Myths and Legends that certain Egyptian texts even went so far as to outright replace Set's name with "Baal" in some cases. The Typhonic name "BOLCHOSETH" is also evidence, since it means "Baal who strikes as Set."