Hello friends,
I was planning on joining a 3 week tour via Intrepid Travels, however my job did not approve my time off (will only approve 2 weeks at a time, apparently). Anywhoo, I am DETERMINED to plan my own similar trip, but cutting it a week shorter. I'll be traveling alone so will be very mobile.

Here is my first draft itinerary:
Day 1 Dubrovnik Croatia
Day 2 Day trip to Mostar (Bosnia) from Dubrovnik
Day 3 Kotor Montenegro
Day 4 Tirana Albania
Day 5 Day trip to Kruja (Albania) from Tirana
Day 6 Skopje North Macedonia
Day 7 Day trip to Ohrid (N. Macedonia) from Skopje
Day 8 Day trip to Prizren (Kosovo) from Skopje
Day 9-10 Athens, Greece
Day 11-13 Santorini, Greece

I know it's a fast paced trip, but I like those even if I just get a taste of the place. Any suggestions for how to travel between these locations or just general advice would be greatly appreciated!

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It's easier to judge if you think in terms of how many nights you have in each place. Are a bunch of these one-night stays? If so, it's a lot of traveling with little time in each place. One-night stays give you a half day or less. Two nights in a place will give you only a day to a day-and-a-half in that place. By the time you check out of your hotel, get to the train station (or airport in the case of Greece), travel to the next stop, get to the next hotel and get checked in, all that takes more time than you might think.

With two weeks, focus on one country, two at the most. Two weeks gives you a good amount of time to explore the Croatian coast, for example, starting in Zagreb or Split and working your way down to Dubrovnik. Adding a day trip or overnight to Mostar and / or the Bay of Kotor is possible. We’re in Greece right now and are taking two weeks to cover just Athens, Delphi, and the Peloponnese Peninsula. I travel fast too, but with one or two nights everywhere, you won’t really get to enjoy much.

go look at rome2rio

don't trust that all their data links work, but it gives you an idea

BTW when will you be having a holiday to recover?

The bus ride from Dubrovnik to Mostar and back lasts about 8 hrs. First arrival from Dubrovnik at noon. I don't think that you will find a bus for going back in late afternoon. But you can of course book a private transfer.
Or take the 17.35 bus to Trebinje ar 21.00 and go on from there by taxi (22 km).
The bus ride from Kotor to Tirana (ar 14.00) takes about 6 hrs. The visit of Kruja doesn't need a full day.
Skopje bound buses (6 hrs journey) leave Tirana at 5am and 5pm and pass through Struga, a few miies from Ohrid.
For Ohrid only, you may take any minibus from Tirana to Pogradec (rather frequent) and go on from there by taxi.
Tirana - Prizren by bus takes 3 hrs. 3 daily departures.
The only direct Prizren bound bus (2 1/2 hrs) leaves Skopje at 4pm. Otherwise travel via Pristina.
Skopje - Thessaloniki: 4-5 hrs, 3 connections daily.
Thessaloniki - Athens: 6 hrs by train.

You may also check the following itinerary:
Tirana - Prizren - Pristina - Skopje - Ohrid - Bitola (all by bus) - taxi - Florina - train - Thessaloniki - Athens.
Direct flights Thessaloniki - Santorini almost daily.

BTW: I suppose you know that you will bypass almost all gems along your itinerary

Bus tours often are very intense, with one-night stays, drive-by stops, and half-hour photo ops. Trying to duplicate such a trip on your own, in even less time, is difficult and exhausting. On a tour, your transportation to the next destination is waiting for you at the door of the hotel, and you don't have to make connections while dragging a suitcase. You can leave everything on the bus when you make a short stop.

One-night stays are particularly tedious when you're travelling independently. If you have only one night in a hotel, you'll have to find something to do with your luggage on the day you arrive or the day you leave, and that might be the only day you'll have to visit the city. A hotel will usually hold your luggage before you can check in, or after you check out; or you can often store luggage at a train station, but these solutions waste precious time.

On a tour, you don't worry about getting on the wrong train, or misunderstanding a schedule, or travelling a distance to see something that turns out to be closed that day.

When traveling independently, it's better to slow down your pace considerably.

For 4 or 5 days, you can go pretty fast, but not continuously for two weeks. By day 6 or 7, you will be forgetting what rail stations you are in.
As pointed out already, trying to do independently the same trip as a bus tour is almost impossible because travel time on your own will be longer and more complicated.
Is day 1 your arrival day?
Is day 13 your departure day?
For you, it would be good to lay out your trip with travel times, including getting from hotel to train station, etc. Do not underestimate times. Days 9 & 11, for example will eat up an enormous time in travel.