Hi,
Some comments on this whirlwind trip: In my younger days I could have seen myself do such a trip within nine days but minus a couple of countries. It takes precise planning to get to specific things/museums/sights you want to see, Come back for the rest on the next trip. In some ways I have done what you have in mind, get to a town/city without the intention of visiting that city but to see one sight or museum, forget the rest of the city. That's what I did in Duisburg, among other towns, hit that city just to see that one museum.
Brussels to Berlin by night is very easily done. Take the regional train to Cologne, then the CNL night train to Berlin. Then if you want to leave Berlin that very night for Austria, say Vienna, also quite easy. The shorter route goes through CR. on the Berlin-Vienna EN night train. That depends where in Austria for you after Berlin. If you want western Austria, say Salzburg, the route I suggest is via Munich, a better night train too since the Berlin-Munich night train is a CNL., then transfer to Salzburg.
On taking those night trains, the cheapest way is just to sit in a six seat compartment, where it's mandatory to have a reservation. You sleep upright, everyone else does it, your compartment mates. On the CNL train you have the choice of a reclining seat or a compartment seat. Any sleeper or couchette is going to be pricey. I wouldn't pay it.
On the WC facilities, many of the big cities in Germany have Rail and Fresh, the best public WC facilities I've seen in train stations, such as at Munich Hbf. The left luggage facility at Berlin Hbf (main station) is next to the WC facility, very handy.
On the accomodations when you don't take a night train, stay at the hostels near the train station, ie, 2-3 mins walk, such as In Paris, London, Frankfurt, Munich, Berlin, Vienna...all have hostels within that distance from the train station. Or, at small hotels there, plenty of them. I don't like relying on a taxi or public transportation to get back to station on the day of departure.