I don't know the technical terms for most of this, but I can explain how the sentence breaks down.
I think the confusion mostly comes from all the parts being separated by commas, when they're actually connected in different ways. The comma is the Swiss Army knife of punctuation marks; or perhaps the universal glue.
It's actually quite common in fluent speech to glue lots of ideas together as we think of them, without paying attention to how long the sentence is getting.
This is a phrase on its own, introducing the whole sentence. It basically means "pay attention to the rest of this sentence". We could perhaps use "Note: " instead.
, because English orthography,
This is a parenthetical, or aside - it's an extra detail that's kind of optional. We could perhaps mark it with dashes or brackets rather than commas. Alternatively, this could have been the start of the sentence, if the "note that" wasn't already there.
There's an extra possibility for confusion here in using "because (noun)" which would more traditionally be "because of (noun phrase)". (I am reminded of Gretchen McCulloch's book Because Internet.)
there are two verbs tear
This is actually the core that all the other clauses have glued onto. It could be clarified a bit by adding quotes around "tear".
There's also an implied "which are spelled" connecting "two verbs" to "tear" (we know it's about spelling rather than anything else from the following phrase).
, pronounced differently
There's an implied "which are" here, connecting to the "two verbs" in the previous clause.
This is actually the first of three different details about those two verbs, which are all basically on an equal footing. We could perhaps use a colon to introduce the list of details, and a semi-colon to separate the items in it.
, one transitive, one intransitive
The second detail about the two verbs. Note that the comma in the middle here isn't separating two clauses, but standing in for "and".
, with completely unrelated meanings.
The third detail about the two verbs.
So without changing any of the wording, only punctuation, we could have:
Note that (because English orthography) there are two verbs "tear": pronounced differently; one transitive, one intransitive; with completely unrelated meanings.
Or taking more liberties with the phrasing, but keeping the same order:
Note: Because of the complexity of English orthography, there are two verbs which are spelled "tear". They are pronounced differently; one is transitive and the other intransitive; and they have completely unrelated meanings.