Where is the root morpheme in Modern English abortion?

It sounds like you've already answered this question for yourself from the etymological point of view.

With regards to modern English, I wouldn't consider the ab- prefix to actually be a productive negative prefix of any kind. In the case of abduct, it's hard to argue that ab- is a negative prefix at all, especially since the stem duct is not obviously related in English to the meaning of abduct. You have to know Latin to make that connection. In the case of abnormal the ab- prefix does attach to an existing word normal, but its meaning here is simple lexical idiosyncracy.

So it is with abortion: I would argue that the stem abort is morphologically simple in English, with the Latinate prefix ab- being an unanalyzable part of the stem from a synchronic point of view. (And most English speakers have never heard of the word ort, and certainly wouldn't connect it in any way to the word abort.)

Ort is an archaic word that means "a scrap or remainder of food from a meal." It derives from the Middle Low German orte ("food remains"), which originally was a compound word related to eat.
Ab- is a suffix that comes from Latin, that in English means "away; from."

In Modern English, abort is not composed from ab and ort.