So this point of frugality etc has been solved?

As also been told to you: between Sof and Split/Zag it will be mostly BUS=extra expense.

There are tons of various forums and blogs about the apparently all extremely unique virtues of even the most mediocre tourist-or less so-towns. Tripadvisor.com is the best known-about every minor possible query has been treated there. For youngers: inyourpocket series does mostly East-EUR, a big part of your trip, which again seems mostly a capital collector. Perhaps your library still stocks a slightly older LonelyPLanet guidebook-except for the prices still an old-style goldmine of that info-and very much aimed at people like you. They also once did a very knowledgeable and funny forum-thorntree- but that has gone down the drains when aunty BBC took it over for way too much money.

My 2 cts would be-as I now count 15 stops (some like Mostar, only that bridge=see in 22 mins): Assume the binge-drinking BG coast will mean a longer stop for rest.

put in PL in between Berlin and go to CZ. Krakow is a must see and very affordable too.

Exchange some of those capitals for other places: B´lava has very little to see (unless you have a special like for old style trams&trolleybuses-but most other east-eur cities have these also a plenty), do the Tatra/Poprad. Do a more local stop in HU (Szeged, Debrecen) and RO (towns like Cluj-Brasov-Sibiu are far more interesting as brutal Bucuresti). Stopover in Ploiesti a few hrs on the way to Buc: get a glimpse of how nasty and ugly those east-EUR communist places once were away from the renovated tourist path. Oh-they also tend to be much cheaper!

BG: Gabrovo, Veliko Tarnovo and/or Plovdiv (has one of the best and loveliest hoStels I ever stayed-though myself not in the dorm anymore) halfway between the coast and Sofia.

In general though specific touristy non-rail/train questions tend to attract only very little response here-understandable.

A lot of your Balkan destinations might be scorchingly hot in Summer. Your plans are a bit city heavy. You might want to find places with nature to cool off ;) 

If you're in Slovenia, I can really recommend the lake of Bohinj (get off in Bohinjska Bistrica), at the footsteps of the Julian Alps and Triglav national park. There's quite some tourism, but much less en more respectful for the local environment in comparison to overpopular lake Bled.

There are free busses to get you to the lake and the mountains.

Spend a whole week there last summer, and really enjoyed all the hiking possibilities, swimming and outdoor activities you can do there. You might want to book early to find a nice self-catering unit. 

I’m aware that it is very city heavy - but it’s only a guide I’ve set out for myself as a general route because I am not particularly well travelled enough to know great places. I will openly take your Slovenia recommendation in my notes. 
 

I am also very inexperienced in the heat due to where I live - do you have any other recommendations along the Balkans to deal with it? I am happy to bend on my route as it’s not very strict.

I’m also not super well travelled in the Balkans, I usually go to old-school travel shops asking for hiking maps or books and any recommendations in the country you want to travel.

Or just check where there’s a national park or natural area more or less accessible by train. Than I google directly. Always nice stuff to find, without being overly touristic or and some place loved by a lot of locals.

I have difficulties to cope with heat (temperatures in excess of 30°-35° c). Do your activities outside early in the morning and late in the evening. Stay cool during the hottest moments of the day. Stay inside, keep everything closed and ventilate only when outside is cooler than outside. Or find a place to cool yourself, in water, a cave, or go higher up in the mountains where it’s cooler, find something with plenty of shade. Avoid too much physical activity anyway and environments that are full of concrete and asphalt.

And keep a half eye out for forest fire warnings, but all depending on the weather of course .

Just keep in mind the Railroutes on the balkan are limited Currently no train Service between Sofia -Belgrade (as Serbian rail upgrades their Network arround Nis)

Belgrade - Sarajevo havent seen a train since several Years :/
Sarajevo - Mostar hey finally a train and its a scenic Route and quite modern Rolling stock (i prefered the old one)
Mostar - Split is again without any train service so here is the Bus a good option.

Keep in Mind Switzerland is expensive, My experience is to search for a Cheap Hostel near Olten (not much to see), Zürich or Bern as these Cities are good bases to explore Switzerland by train due the good  rail connections. 

Regarding nature i recommend aswell Slovenia (Predjama Castle, Postjna Cave Park to be added) :)

another nice Spot could be Dresden or Bad Schandau between Berlin and Prague with the Saxon Switzerland (Germany) and Bohemian Switzerland (Czech Republic)

I usually visited Bratislava as daytrip from Vienna :)
If iam on a tight budget i did it quite opposite and stayed in Bratislava and took then the 1hr train Ride to Vienna :)

From Berlin you may have a daytrip to Potsdam (Bridge of Spies “Glienicker Brücke”, House of Potsdam Conference, Schloss Sansouci) maybe combine it with a nice ship tour from Berlin Wansee  to Potsdam :)

Between Budapest - Bucharest i recommend a Nighttrain or you plan a stop inbetween (Quite long Trainride). From Varna to Sofia you can use a cheap Bulgarian Nighttrain :)