Iran is a very safe country to travel, probably much safer than the United States... Syria, I agree with you, is another matter, and for the moment, no trains are running there anyway, even no trains to the closest big city in Turkey, Gaziantep.
I first saw mention of the Trans-Asia Express when I visited Istanbul with my wife in 2005. In the Haydarpaşa train station there was a map showing this train journey, and having seen it, I was sure that one day I would do it.
So in 2009 my wife and me departed Brussels for a train journey to Tehran, prelude of a 3 weeks stay over there. There was of course nothing like a direct train to Istanbul anymore, so the itinerary was:
- Day 1 ICE train to Köln
- Night 1 Sleeper to Munchen (in those DB double decker sleepers, awful)
- Day 2 ÖBB Railjet to Budapest
- Night 2 Sleeper to Bucharest
- Day/Night 3 Sleeper to Istanbul
We had a 2 nights buffer time in Istanbul and then we set off to Tehran with the weekly Trans-Asia Express.
After a visit of Tehran, we went by road to Shiraz (Persepolis!), Ispahan, Yazd, and Kerman.
At that time, Kerman was the easternmost point reached by the long distance trains from Tehran. The line to BAM was already open, but served only by local trains. We did not go, because of the earthquake that devastated that city a few years before. So from there, we took an overnight train to Mashhad, and then an overnight train again to Tehran for our flight back to Brussels.
What I meant is that once you are in Iran, you don't have much options to continue further East, unless you are very adventurous:
- Now that the line to Zahedan is open, there is this bimonthly train to Quetta, which is nothing more than a basic passenger car hooked on a freighter;
- And from Mashhad, you can take a train to Serakhs, at the turkmen border, cross the border by foot, and then take a turkmen train to Ashgabat.
None of those options are very civilized and although I dream to go by train to India some day, I doubt very much it will ever happen. But who knows?
Regarding your other question, yes there is a rail border crossing between Greece and Turkey, in Pithion, as
LNW-GW Joint just explained. Until 2011, there was a daily night train between Istanbul and Thessaloniki that used this border crossing. Sadly, OSE cancelled it as a cost-cutting measure and it was never re-instated. There were two train sets, one turkish using TVS2000 coaches, and a greek one using second hand Wagon-Lits from SNCF. If it ever comes back, it will be my next trip.