"Are YOU coming to get me" / "Are you coming to GET me" Is there any grammatical or semantic difference?

You're asking whether the sentence is ambiguous, and whether the ambiguity is in pragmatics or semantics.

Pragmatics is a subfield of linguistics and semiotics that studies the ways in which context contributes to meaning. Pragmatics encompasses speech act theory, conversational implicature, talk in interaction and other approaches to language behavior in philosophy, sociology, linguistics and anthropology. Unlike semantics, which examines meaning that is conventional or "coded" in a given language, pragmatics studies how the transmission of meaning depends not only on structural and linguistic knowledge (e.g., grammar, lexicon, etc.) of the speaker and listener, but also on the context of the utterance, any pre-existing knowledge about those involved, the inferred intent of the speaker, and other factors. In this respect, pragmatics explains how language users are able to overcome apparent ambiguity, since meaning relies on the manner, place, time etc. of an utterance.
The ability to understand another speaker's intended meaning is called pragmatic competence. - wikipedia

Since your sentence is identical in both instances, syntax and grammar are the same. The semantics can be different, depending particularly on the meaning of get (get=fetch or get=assail). However, even if we take get to mean fetch as your question implies, the pragmatics are different.

If you don't know who is going to fetch you, then your first interpretation makes sense, with a stress on the word you in the sentence. If your enquiry is about whether the person is coming to get you at all, the stress is on are or coming. Stressing other words leads to other interpretations.

So to answer your question, yes, it's ambiguous, and the ambiguity lies in semantics and pragmatics.

Depends what one means by grammar. The grammar books of my schooldays would cite a sentence like "Are you coming to get me?" as an instance of stress or accent.

I've read somewhere that the early British phonetics buffs argued that accent was somehow grammatical, but our writing systems were so deficient that we could hardly recognize or comprehend its system. (Eventually such disciplines might coalesce, and a more abstract, but cleaner and better grammar would emerge.) Older books file accent with elocution, half of the art of which consisted in attempting to correctly infer probable accents in texts (where no accents were recorded) that would be otherwise obscure or unintelligible.

In 2016, what discipline claims the territory of accent? On this page Lawrence plants flags for linguistic pragmatics and semantics. Supposing these to be on very firm ground, this knowledge should naturally trickle down to improve our society. In 2016 we have sophisticated artificial languages created for fiction and TV shows, but our national rulers are not notably more eloquent, and a general unintended obscurity fuddles forth.

Maybe in 3016...