Clearing in and clearing out of a country is far less problematic as led to believe; difficulties are mostly self-inflicted:
1. Inform yourself about required documents, this is usually an internationally recognized ship-document, proof of
insurance (the European "blue card"), crewlist, passports of all crew with valid visas if required and (if required by home-country of the vessel)
license of the
skipper, including VHF/shortwave-license if you have
radio... you are set. Europeans do not carry
guns, preferably do not bring any, if you think you must: declare them and have proof that you carry them legally, most likely they will be confiscated for your stay in the given country.
Some Americans find all this complicated... ever thought of what a foreign national has to go through to enter American waters...
2. Some countries (Croatia, Montenegro, Greece and others) charge for the right to use their waters, be aware of it, accept it and pay the fee or sail elsewhere.
3. Read handbooks, use official port of entries, know where the customs-dock is, where the police and the harbor-captain's office are. I had sailors complaining about "harsh treatment" after making landfall in a harbor that was not port of entry, this is like crossing a border illegaly, do not complain about problems after that.
3. Have all documents well organized when clearing in/out.
4. Treat officials with courtesy and respect; YOU are the guest here. If they give you a hard time... being rude in return will only make it worse. If they do not speak
English, ask yourself, how much of their language do you speak...
5. Clearing in/out between Turkey and Greece is just like any other transition as long as you follow the rules. There are hundreds of yachts transiting between the two countries, particularly the
Greek islands of Lesbos, Chios, Samos, Kos and even Rhodos are so close to Turkey that even
Charter boats frequently leave Greece for Turkey and vice versa.
6. Patras would likely not be your port of entry; by international maritime law the
skipper should use the first port of entry after entering territorial waters, not the one that is most convenient unless an
emergency dictates otherwise; arriving from
Sicily your port of entry is likely Zakinthos (Zante).
Te Kyklades and Dodokanes are among the nicest sailing-areas; enjoy it.