I definitely understand the distinctions now, but to clarify:
A) Non-recognition of autocephaly does not necessarily imply that two churches are not in communion?
Yes, it does not mean lack of communion.
B) What churches do not recognize, currently, the autocephaly of certain others?
At present IIRC, the only one now that is not universally recognized is the Orthodox Church in America. Constantinople, Alexandria, Jerusalem, Cyprus (i.e. the Greek Church) oppose its autocephaly, and officially see it as part of the Russian Orthodox Church, at least until last year. Last year at the Episcopal Assembly Constantinople implicitely recognized it as not part of the Russian Church and autocephalous, but explicitely avoided officially doing so. Moscow, Bulgaria, Georgia, Poland, the Czech Lands and Slovakia recognize it as autocephalous. Antioch, Romania, Serbia, Albania do not recognize it, but do not question its canonical status. Bishops of the Greek Church, the Antiohican, the Serbian and Albanian Churchs have taken part in the enthronement of the metropolitan of the OCA, however. Only Jerusalem and Cyprus have not ever had official contact that I know of with the OCA.
C) Are there currently Orthodox churches not in communion with one another?
There are ones, like the "Genuine Church of Greece" (claims to be the real Orthodox Church of Greece) or ROCA (which claims to be the Russian Church, not to be confused with ROCOR, which is in communion with the Russian Church and everyone else); and those who are in schism, like the alternative patriarchate of Bulgaria (which does not recognize the Bulgarian patriarch); and those who have proclaimed their autocephaly and gone into schism, like the Ukrainian Orrthodox Church-Kiev Patriarchate (not to be confused with the UOC-Moscow Patriarchate, which is in communion with everyone) and the Macedonian Orthodox Church (which is in competition with the Serbian Church's Archdiocese of Ohrid, which is in communion with everyone). Then there are some groups like the Milan Synod, who originate from schismatic groups. These groups are not only not in regular communion with us, but are not in communion with each other.
There are also the Oriental Orthodox (Coptic, Syriac, Armenian, Ethiopian, Indian) who are not in formal communion with us, but are in full commuion with each other, have signed communion agreements with us in Egypt and Syria, have informal communion with us, and who hopefully one day soon will be fully in communion with us. The issue here is that they formally do not accept the Ecuemnical Council of Chalcedon, and subsequent issues that that entails.