night train booking to get the InterRail discounted tickets is not possible to do online in Eastern Europe.
but I recommend the international ticket office for train tickets (it is run by the Bulgarian railway company) at Sofia main station. it is in the left corner (coming from main entry) - beside the "night train office/lounge". they have nearly everything for Eastern Europe. just be nice and smile to the old ladies there. Sofia - Skopje
is one of these trains, depends at what time you travel (just click at the schedule planer on the train number to find out departure and final destination - so you know which train you will use):bucharest-istanbul-night-train-t1639.htmlsofia-belgrade-vienna-night-train-t1847.html
(you can compare the fares with this train as it is also a Bulgarian night train)
Skopje - Belgrade:thessaloniki-skopje-belgrade-night-train-t1636.html
or a free day train.