The Ottoman Censuses are some of the most contested documents in modern Middle East history. 1893 was a product of multiple years of survey. I can't remember if the 1899 census was a separate enumeration (I think not), but the 1906 census was not a separate enumeration, but instead a statistical update of the last enumeration taking into account models of natural growth. These censuses, we should be clear, do not take into account our national categories (Greek, Serbian, Albanian, Turk, Arab, etc) but used the legal-religious categories of the Ottoman State (Muslim, Orthodox Christian, Catholic, Protestant, Armenian Apostolic) such that by the end of the empire, what we call today simply "Armenians" were divided into three different millets (Apostolic, Eastern Rite Catholic, and Protestant if I recall correctly). In addition to the official Ottoman censuses, there were also completely separate attempts at enumerating or estimating the population of Christians in Eastern Anatolia done by the various patriarchates. These make an argument that the official census systematically underestimates the number of Christians and overestimates the number of Muslims. Most historians in the West agree with these assessments, but don't adopt the Patriarchates numbers wholesale. The best living authority on the Ottoman census is Justin McCarthy (who is a highly controversial scholar--he's the most prominent Western scholar who pointedly refuses to use the term "Armenian genocide"), though Stanford Shaw and Kemal Karpat have also written influential articles on it. The Ottomans also conducted smaller census on certain subgroups for other purposes, those mentioned above are just the national censuses. Anyway, my only point is it's unclear where those numbers come from, and how much to trust them.

Anyway, before we get to the Greeks, lets deal with the rest of the map. There are Muslim majorities in Bosnia, Kosovo, and Albania to the present day, and a large Muslim minority in Bulgaria (both Turks and Slavic Pomaks), where they're over 10% of the population despite massive emigration in the 80's and 90's to Turkey, and Macedonia (both Turks and Albanians), where they form ~25% of the population--some of whom are even fighting for independence a la Kosovo. Muslims have a rather small presence in Romania (less than 1%) and the other states of the former Yugoslavia (~3% in Serbia not including Kosovo, about ~1% in Croatia). So, this is just say, a lot of the descents of those Muslims on the map are still right where they were.

However, not all of them are. I've seen various estimates, but I've seen estimates of 250,000-500,000 Muslim refugees came to Anatolia as a result of Ottoman losses in the Balkans culminating in the two Balkan Wars (1912-1913). Then, in the aftermath of World War I, Greece sought to expand at the same time that Turkey sought to transform into an ethnically-based nation state ("Turk" had no legal meaning in the Ottoman Empire, only "Muslim"). I wrote about this period from the Greek perspective in this older answer. Anyway, in 1923, after the current borders of Turkey/Greece and Turkey/Soviet Union (including Armenian and Georgia) were formally negotiated, there was a massive population exchange negotiated between Greece and Turkey. About 1 million Anatolian Christians were formally made citizens of other states (historians argue that many to most had already fled either to Greece or eastwards, joining other parts of the Greek or Armenian diaspora in places like Lebanon, Syria, Soviet Armenia, Iran, etc) while a little less than a half million Muslims in Greece. The exchange was based on religion, not language or anything else, so Greek speaking Muslims would end up in Turkey and Turkish speaking Christians (whether Greek or Armenia or otherwise) would in theory have to leave Turkey (there is a small Syriac population around Mardin and Midyat, and a mixed Christian population in the Hatay province which joined Turkey after the exchange). There were two areas that were formally exempt from this exchange: in Turkey, Istanbul and Eastern Thrace (where there is still a large Armenian population, but most of the Greeks have left, in large part because they were targeted every time Cyprus heated up), and in Greece, Western Thrace. Muslims still live in Western Thrace, where they make up ~1% of the total Greek population.

Almost everyone else went to Modern Turkey. I have a friend from the city of Mersin on the Turkish Mediterranean coast. She has particularly kinky hair and skin that's on the darker side for a Turk. It didn't seem noteworthy to me, but she once pointed it out to me and goes, "You know my mother's side of the family is from Crete, right?" I go, "Uh, okay..." and she goes, "...and that a large part of the Muslim population of Crete were Black former slaves?" There is, in fact, a small Afro-Turkish minority that has similar roots, but less intermarriage with the general Muslim population of Turkey.

It's been widely observed that a plurality of the Young Turks leadership (using Erik Jan Zürcher's expansive definition of the "Young Turk period" going from 1908 all the way to 1950) were from these mixed Greek-Muslim-Slavic places that ended up outside of Turkey. If we include mixed Greek-Turkish places that Greece wanted but ended in Turkey (that is, Istanbul and the Aegean Coast), a majority of the Young Turk leadership had this background. See Erik Jan Zürcher's Young Turks: Children of the Borderlands? for more. The general mass of Muslim refugees from the population exchange as well as previous refugees from the wars of in the Balkans and the Caucasus, however, just became "regular Turks". Ataturk himself was from present day Greece, and did most of his education in present day Macedonia. Ataturk, and his whole circle, even though many of them came from present day Greece and Macedonia, romanticized that idea of Anatolia as their homeland and completely abandoned any recognition of their Balkan roots. To give an example of how deep this goes, Nazim Hikmet, a famous Turkish poet, a Communist and internationalist who died in exile in Moscow, wrote in his poem "Testament" ("Vasiyet"):

Comrades, if I am not granted to see that day; If I should die before freedom comes: Lift me up and carry me Bury me in an Anatolian village cemetery.

That may seem like a nice little piece of nostalgia from his youth or something, but Hikmet was born in 1902 in what is today northern Greece, in the city of Salonica, and did not even visit Anatolia until he was 18.

So, in short, what happened to this large number of Greek Muslims (the majority of whom spoke Ottoman Turkish as their mother tongue) is that they became Turks.

If you want some info from a some what modern perspective here is some information of Greek Muslims living in Greece at the current time. Excluding Athens which mostly has modern refugees or immigrants, the vast majority of the muslim community that stems from Ottoman rule lies in the areas near Turkey in the Greek region of Thrace. The areas of Xanthi and Evro have a significant amount of Muslims living in those areas and they refer to themselves as Turks.

I served in the military in that area and had some friends who identify themselves as "Turks" not Greek Muslims. From a historical perspective the original Turks were the Seljuks but the vast majority of the Turkish population today are descendants of Greeks that converted to Islam. This still applies today to their identity in Greece, those Muslims from Xanthi or Evro are Turks who did not leave during the population exchange.

There is an even a tv show on Greek tv now about Turks or Muslims in Greece that live in Athena but came from Xanthi called [TAMAM] (http://www.antenna.gr/minisites/tamam/). The Dad is Turkish and the Mom is Greek, both are divorced with kids and get married.

Anyway to answer your question, you could look at this [map] (http://en.wikipedia.org/wiki/File:DeportaLausanne.jpg) it is from wikipedia but it comes from the [Hellenic Resources Network.] (http://www.hri.org/forum/diaspora/turkey/krypto1.html) It doesnt answer all of your questions but the map says that 25,000 Turks left from Crete and 360,000 left from Macedonia.