Vienna-Krakow should be possible via tickets.oebb.at via seat only option (3€), maybe booking is not opened yet, Poland opens booking so 90-30 days before. 

Krakow-Bucharest: First train is of Leo Express, you have to reserve via Leoexpress.com with the discount code Interrail. (I tried now to book, and it says 10,80€ for a reservation. This is expensive for middle-eastern Europe). Prerov-Breclav reservation free and Breclav-Budapest Nyugati reservation optional. ATTENTION 2 other stations in 2 different places in Budapest!!!

Budapest-Keleti-Bucuresti Nord is reservation compulsory. 

I would suggest to use this train (or you visit Budapest as a stop in your tour): Reservation for Budapest Kelenföld-Bucharest is possible via tickets.oebb.at with the ONE WAY TICKET option, and adding as discount Interrail/Eurail Globalpass. For the leg Krakow-Budapest should be possible via cd.cz searching the trip and clicking on I want only a seat. At the moment not possible, maybe to far away or not possible via CD? You should be able to reserve at a ticket desk in Poland. 

Bucharest-Istanbul. There is a nighttrain from Sofia to Istanbul Halkali. But CFR calatori on the website would sell me as a direct train from Bucharest to Halkali on the same time. I can’t find only reservation on the website of CFR calatori. cfrcalatori.ro 

Maybe @seewulf know more about this?

Buc-Ist: only 1 couchette car, shunted from train 1-2-3 to the main train from Sofia-ends some time in sept-exact last date not yet known or unclear. Most people say that out of season (assuming it still runs then) always space available on the day)

Online RES via CFR is fraught with all kinds of difficulties

Hi, that’s really helpful thanks! 

• The Vienna - Krakow works well thanks
• The “Reservation for Budapest Kelenföld-Bucharest is possible via tickets.oebb.at” didn’t have many options but I managed to find a reservation on the interrail site but it was a bit expensive, but I have that now. 
• If anyone knows whether the Bucharest to Istanbul train will be running on the 13th of September it would be really helpful… I couldn’t seem to book it through the CFR

What do you mean with didn’t have many options but I managed to find a reservation on the interrail site but it was a bit expensive, but I have that now. 

Did not work the ÖBB website?

It only seemed to let me book a seat for one of the trains times (which was not convenient for me) but not the others. Maybe it was something I was doing wrong, anyway I have booked that leg of the trip and thanks for the help.

If you know anything about the Bucharest to Istanbul train it would be great!