I haven't been to Macedonia, and Mostar/Athens/Meteora were a very long time ago.
In general, rail service in the Balkans is limited and slow. Very slow. You will in many cases find your best (or only) choice is buses. On my 2015 trip to Montenegro, Romania and Bulgaria I figured I covered about 30 mph. And distances are not particularly short. Therefore, this area is not great for hub-and-spoke travel.
An example: If you want to travel from Romania to Bulgaria by train, you'll probably have to get to Bucharest first; Bucharest is not one of my favorite places in Romania, but I couldn't avoid it. The rail line from Bucharest, Romania, to Sofia, Bulgaria, crosses the border at Ruse. Travel time by train just for the Ruse-to-Sofia segment is 6-1/2 hours. Sofia, as it happens, is far from my favorite place in Bulgaria. I would recommend Plovdiv and Veliko Tarnovo instead. V.T. is about 3 hours from Ruse by train. V.T. and Plovdiv are about 140 miles apart. Buses apparently take 4 to 5 hours (I don't remember; that's what the extremely unreliable Rome2Rio.com says). Trains takes about 7 hours or more with two transfers.
That's more or less the way it goes in the Balkans. With a willingness to get up early in the morning and perhaps take the occasional taxi between towns, you might be able to see most of these Romanian sights (all of which I recommend) from a single base: Sibiu, Brasov, Sighisoara and Peles Castle. You'd need to dig into bus schedules as well as train schedules, and you'd probably be spending 4 to 6 hours for round-trip transportation to reach each destination.
Romania is a really fascinating country and could keep you busy for considerably longer than 2 weeks, even if you rented a car. The Retro Hostel in Cluj-Napoc (a city with a very attractive historic area) arranges day-trips and longer excursions. You might check out its website. I took the excellent 2-day tour to Maramures even though I was not staying at the hostel.
Montenegro could be combined with Dubrovnik and perhaps Mostar. You'd probably not set foot on a train. Montenegro is small enough that it is possible to pull off some day-trips. I stayed in Podgorica (recommended only because it's a transportation hub) and Kotor, and I was also able to see Ulcinj, Cetinje, Budva, and Herceg-Novi, all by bus. The national parks, which I understand are lovely, appear to be totally inaccessible via public transportation.
As far as I know, rail service between Athens and Bulgaria is so slow and infrequent as to be virtually non-existent. It appears that buses take over 12 hours. To combine Athens with points north and west on a short trip, you really need to fly. The Wikipedia page for the Athens airport will list the destinations reachable by non-stop flight from Athens. Note that some of the routes may not operate every day. Routes that are seasonal will be so noted, but "seasonal" will not be defined.
To explore the transportation options between places of interest, you can start with Rome2Rio.com, but do not under any circumstances trust the fares, travel times or frequencies shown on that website. Instead, you need to keep drilling down until you find the names of the train and/or bus companies offering service on the specified route. Most of the time there will be a link to the companies' websites, where you should be able to get reliable information, at least for the current time of year. It may not be so easy to find schedules for next spring/summer right now.
It might also be worth exploring the Seat61.com website. It has information on train service all across Europe.