Istanbul to Vienna by rail

http://www.sas.com.mk/en/VozenRed.aspx

This is the Skopje bus terminal site and it says there is a bus most days of the week to Tirana,Durmo Tour,leaving at 6AM,taking about 7 hours.
They should be big buses that you travel on,but they may have luggage restriction weight for people,just offer to pay a bit extra to get your luggage on if they say anything.
For Istanbul-Sofia,there are plenty of buses leaving from the main bus station [Otogar],I suggested Matpu because it drops you in Sofia right outside their office and you can just go in and get your ticket to Skopje,because they are one of the companies that do the Macedonia lines.In Skopje there is a big bus station where you can buy your ticket to Tirana,Durmo Tours should have an office in the bus station,have to check on that,or you might be able to buy from the cash desk in the waiting area.
If you want any help with accommodation let me know,and what money you want to pay and if you want to stay near bus stations or you don't mind anywhere,there's plenty of time to find out that stuff.

Hi Chiaka, If you're still available to help I would greatly appreciate it. I was busy and unable to plan this but now I am ready to lock this trip in. I relooked at buses from Sophia - Tirana, and I don't think I will be able to do this route because most buses leave on weekdays and I would be leaving Sophia on a weekend. Let me know if you know of any bus service that would leave sat/sun if you can please. Otherwise, I am thinking to take Durmo tours from Sophia to Skopje. And then skopje to Tirana since there are a lot of buses on this route. What do you think?

Also what's you opinion on accommodation? Are most bus stops conveniently located or will I be taking a taxi to most accommodation?

There is a bus from Sofia to Tirana on Sunday night at 18.30,book it at Matpu office as it is their partner company doing it.Accomodation needs to be sourced close to the bus stations as possible,it shouldn't be a problem once you decide what you want to pay for hotels/hostels/guest houses,so you really need to decide what your budget is for accommodation.

Hi, so I messed up on the dates. Im actually hoping to Leave from Sophia on Tuesday to Tirana, but very few bus services seem to go direct. According to math, they have services twice a week including one on wednesday. Do you know if they have a partner company for Tuesday? Also budget is flexible. The main thing I am wondering is if most bus stops are in the city center where I hope to stay? Or are they usually a little way from the city. I believe the matpu stop in Sophia is close to city center

They are going to Tirana on Wednesday,Thursday,Friday and Sunday.If you hope to leave Sofia on Tuesday,you won't need a hotel as you said you are leaving Istanbul on the Monday,9/7.
Did you buy your bus tickets in advance through that site I linked to?

I have not bought tickets yet I am still figuring out. We are actually leaving on 7-9 in the morning and will arrive by 6 pm in Sophia. We were thinking to take the bus at 7 am on 10-7 to Skopje and then travel from Skopje to Tirana. How does this sound? I believe Skopje is in the middle and I know this is tiring but we want to get to Tirana before we slow our pace down.

Which bus is going from Sofia-Skopje at 7AM?
From Skopje-Tirana there is only the Durmo bus at 6am daily.
You haven't got much time to get everything organised with the tickets for the buses we talked about and hotels.
Probably best to book hotels through Booking.com and get one close to the bus stations.I only had a quick look at the bus stations in the places you are going,so am only guessing that your buses go to these stations,some places in the Balkans have 2 or 3 bus stations,but in Sofia,go for Ramada or Aris Hotels,in Skopje,Astera Hotel,Apartment Hotel,Smart Apartment or New Central Apartment,in Tirana it looks like the buses go from the Bus Station at Asllan Rusi,so go for Hotel Dilo.

In Kotor there is a main bus terminal,in Dubrovnik also,the bus Kolodvor,in Mostar the Iztok Kolodvor and in Sarajevo the Autobus Stanica,so have to look for hotels near them places.

Thank you so much this is so helpful. I will finalize today. The bus from Sofia to Skopje is called KALEIA. Do you know about this? Also I booked a hotel close to the bus stop in Sofia but will we actually have time to see anything for those few hours in the evening? The other option is just staying in Sofia till Wednesday. But that seems like too much time in Sofia and I would rather make progress and go halfway to Skopje.

I know Kaleia,I travelled to Skopje and back with them a couple of years ago and they were not good,really stupid driver,small bus with no room for much luggage,I would never ravel with them again.
In the hours you are in Sofia,you can take a trip up to the Alexander Nevski cathedral,it is well worth seeing.

HI, thank you so much for all your help cant explain how much I appreciate it. Okay i booked something close to serdik station in Sofia which is good right? Then we will go ahead and take matpu to Tirana on wednesday night. Do you know how I can go ahead and buy this ticket? Also I am thinking to take Metro bus from Istanbul to sophia, do you know where their office is in istanbul? having trouble locating information on it. Thanks!