There's no rail connection between Niš and Priština, as well as between Skopje-Tirana, Shkodër-Podgorica and Podgorica-Mostar. I don't know about any regular buses from Niš to Priština, but there are private minibuses.
There are direct buses from Tirana to Podgorica, but if you want to travel on Albanian trains (rough but interesting experience, IR or Balkan Flexipass not valid, but tickets are very cheap), you can go with train to Shkodër, then take a minibus to border village Hani-i-Hotit, on foot or by taxi to Montenegrin village Tuzi and then by regular bus to Podgorica.
Or take a bus from Shkodër to Ulcinj at then go by numerous buses along Adriatic coast. Podgorica isn't so interesting, an ordinary Communist site with a lot of concrete
I recommend rather Cetinje or Kotor.
There's probably no direct bus connection between Podgorica and Mostar, but you can get a bus along Adriatic coast to Ploče and then take a train from Ploče to Mostar and further to Zagreb (I recommend the railway section Mostar-Sarajevo, nice engineering work!)
For bus timetable you can try the Croatian site www.autobusni-kolodvor.com
The private minibuses are often cheaper than ordinary buses, but they don't stop at official bus stations, have no timetable and you'll probably ask local people to get correct info.
I think that Global IR will be probably too expensive variant, because a lot of bus transfers and cheap ordinary tickets. There are cheap e-tickets from Prague to Budapest (cd.rail.cc, 19 €), cheap offer Beograd Special from Budapest to Beograd (15 €). In Beograd you can buy Balkan Flexipass, a network ticket for Serbia, Montenegro, Romania, Bulgaria, Macedonia, Turkey and Greece (www.zeleznicesrbije.com/active/en/home/glavna_navigacija/putnicki_saobracaj/medjunarodni_saobracaj/cene_prevoza_v01.html
, 50 € for youths, 5 days in one month).