を can also be used as an object indicator (本を読むetc)

みみずをたべた。

Not entirely sure here, but wouldn't it be better to use が instead of を if you're using "the" in the equivalent English sentence?

Well by that line of thought, it's also possible to say in English that you ate an apple, which would be translated into Japanese as the same sentence you typed. I always felt that を did not focus on a specific object, but instead an instance of that object among others. I could be wrong about this, but whenever I heard を I always felt that there was no focus whatsoever on the object, which is what I'd get with the English 'a/an' and not 'the'.

Between my studying of Japanese and teaching English to Japanese people, I would be pretty confident saying that there is no 'the' versus 'a/an' in Japanese - trying to teach that concept, it seems pretty difficult to grasp among my students. The を in the sentence ミミズを食べた denotes that the earthworm is the object of the sentence instead of the subject - ミミズが食べた would mean 'the/an earthworm ate'

Probably a sentence where an understood part of it was cut out for convenience.

Yea, you could technically argue that it is a subset, but I think keeping them separate simply helps more clearly show the different ways that it can be used.

Yes, that's correct - the "through" or "over" or "along" translations apply only to verbs of motion. A couple examples: 橋を渡る - this one's pretty unambiguous; you can't use 渡る with the "in" or "at" meaning of で, in the same way that you wouldn't say "I crossed in the bridge." You could, I suppose, say something like 箸で渡れる島, where で means "by means of" (an island that can be reached by bridge), but this is really a different application. 公園を歩く - in this case, the use of を means that you're walking [i]through[/i] the park - it's not your end goal, you're just passing by en route to somewhere else. 公園で歩く would be "I walked [i]in[/i] the park," and in the case, the focus is on walking as an activity - you're going for a stroll around the park, without a definite goal in mind.

I've noticed an usage from DoBJG is missing, page 352: "A particle that marks the cause of some human emotion"
examples:

次郎は父の死を悲しんだ・悲しみました。
Jiro was saddened at his father's death.

私は浩の大学入学を喜んだ。
I was happy about Hiroshi's entering college.

Is it worth adding, or I'm suggesting needless complexity? :S