OK, let's try to add some detail and clarification.
No I do not see two Focus in the sentence. and I would not say that "You" is the "Topic" of the sentence/clause.
The very reason that I use "Contextualizing Constituent" for this pragmatic function (a.k.a. Topic) is illustrated in your question. When a piece of a clause is used to relate to the larger context and it receives special marking by being placed before the core of the clause (in Greek that means before the verb), then I call it a Contextualizing Constituent. Traditionally, this is called "Topic" in Functional Grammar, but as you have just demonstrated, that label causes confusion because it will often be interpreted according to its English meaning and not accordingly as a technical term and as redefined. This is especially important to clarify in a language where the word for "subject" and "topic" may be the same. Such a language forces the creation of a technical term that does not mean "topic/subject".
Normally in languages, if two items may be specially marked by placing before the core of the clause, the first item so marked will be relating to the larger context and is a Contextualing Constituent while the second marked item will be more salient and carry the most important piece of the communication, a Focus, the point that the sentence was trying to make, and marked. A sentence does not need to have either a marked Focus or a marked CC. They only occur when a default item is given special treatment (marked, non-default). In that sense the word 'marked' in "marked Focus" and "marked Contextualizing Constituent" is redundant and only added sometimes as a reminder these pragmatic items are not default items.
By the way, I assume that in most languages (not all) the difference between a marked CC and a marked Focus can be heard in speech. While both CC and Focus can be marked by word order, being placed before the core of the sentence, the Focus will carry a Focal intonation, too.
Back to John 13:6, it may be read as a reversal of the prototypical marked order:
the SY may be read as the marked, most salient piece of the sentence (Focus, including a Focal intonation), and MOY may be marked secondarily as contextual reference for the sentence (CC, and without focal intonation), in this case providing the more assumed and expected reading "I (would) wash ..."
So the sentence can be read: "you" (surprise, marked Focus) more than "me/my" (expected, marked Contextualizing Constituent) are going to wash feet?
Other readings are possible. For example, one might treat SY as the C.C. and MOY as Focus, but that would require adding a Focal intonation to the fronted MOY, something debated in this thread.
I am caught between two poles on this question. On the one hand I recognize that the Greek accent system was recorded according to rules and not changed for individual contexts so that it is somewhat artificial. On the other hand, where it is possible to read something in accord with the accent system I am inclinded to let it be so read. So here, the enclitic reading of SOY would mean that it is not Focus but a CC. Nevertheless, there are many examples of marked Focus where a default high tone on the final syllable is dropped and written grave because a word follows. If I read such a word as Focus, then I restore its high tone in my reading, even though the written accent is grave. A grave means "potential accent" for whenever the word pops out into its own, something that I claim happens with a Focus pragmatic marking. Technically, if a person were to read a Greek sentence slowly, then all grave accents should be pronounced. They are only dropped (that is, left as grave "no accent") when reading fluently or for Focal readings.