Looking for advice on an Interrail trip starting in Geneva, travelling through the Balkans and Turkey, and on to Italy

As you're stopping for a couple of days in each of the cities, I think you should be able to get some rest from travelling. It is not as relaxing as a resort holiday, but it's also part of the experience. Be aware there are no trains from Turkey to Greece, so you'll have to go by bus. 

I haven't taken those ferries yet.

First question: has anyone taken the ferry (Greece–Italy) before? Specifically, the Attic Group, which has very poor reviews, and Minoan Lines.

I never had travelled by ferry between Greece and Italy.

Another question: most of my journeys are about 10 hours long (I plan to travel overnight). Do you have any thoughts on this (I’m worried I’ll get tired from the journeys)? And also, if you have any general recommendations for my route, that would be great!

Nowadays as senior citizens both my wife and me try to avoid overnight travel by train and if it seems to be necessary only in a private sleeper compartment. When doing interrail travel with friends when I was in my 20s we did occasionally overnight trips. Always in seat carriages, never couchettes or sleepers. We never did this two consecutive nights; at least two or three nights between staying in hostels. I could sleep rather well and had never problems being too tired. Not pleasurable at all was changing trains during the night and waiting for the connection from midnight to 2 a.m..

Probably there will be line closures on your trip due to engineering works. E.g. between Buchs SG and Feldkirch through Liechtenstein. The euronight train Zürich – Zagreb (if you wish to take this one) will be rerouted. Daytime trains are also rerouted or you have to take a rail replacement bus. In Slovenia I would recommend to travel in one direction the Bohinj line Jesenice – Sežana (rail replacement bus service on a part of the line you should expect). If you go from Slovenia to Vienna the Semmering line would be the natural choice.

Thank you for you help!