Itinerary from Sofia to Split
 

I am spending two weeks in the Balkans in June.
I would like to use public transportation for my trip from Sofia to Split.

A first draft of my itinerary would be:
Sofia
Skopje
Pristina
Prizren
Tirana
Kotor
Dubrovnik
Split

I am thinking it might be to tight. Should I remove perhaps Albani?

Suggestions?

Hope your passport has lots of blank pages. :D Balkan twisty bus routes sometimes cross the same border multiple times in one trip -- and you get a stamp at every border stop. Also the buses and trains in that area are very slow. So yes, you have too many stops for 2 weeks. Perhaps you can leave something for another visit.
Btw, one of my favorite Balkan experiences was a visit to Sarajevo.

What are you looking for? Cities, museums, architecture, natural scenery, food, beaches?

I'd probably skip Kosovo instead of Albania:

Sofia - (maybe) Skopje - Ohrid - (maybe) Tirana - Bar/Budva/Kotor - Dubrovnik - (maybe) Mostar - Split

or for something different:

Sofia - Belgrade - Sarajevo - Mostar - Dubrovnik - Split

I like this route (minus Dubrovnik), being a comfortable fit for a 2-wk trip. With Dubrovnik - Cerna Gora - Albania - (something else) taking another 2 weeks.
I suspect this may not appeal to the OP though, being too different from the original plan.