I have the same question.

Without the "que" it's not the same phrase: "ele veio. depois você saiu"("he came and you left.") With the "que" is like "you just left and he came". Sorry, it's very confuse to me to explain, i hope you understand.

Well, where I live we pronounce DE like gee at the end of a word or when it is by itself as a preposition (of). The others are normal "de"

That would be "viu" (also an irregular preterite form), based on "ver" (to see), not "vir" (to come). I, too, frequently confuse the two.