[url=‘http://reiseauskunft.bahn.de/bin/query.exe/en’]DB timetable[/url]

A more logical route would be:
Brussels – Amsterdam – Berlin – Prague
a) Vienna – Munich – Zürich – Venice
b) Munich – Vienna – Venice – Zürich

From Zürich you could use the [url=‘http://www.elipsos.com’]Elipsos Trenhotel[/url] night train to Barcelona.
Otherwise I would check for a budget flight for the trip to Madrid – or even better Lisbon.
http://www.whichbudg…
Somewhere from Switzerland, Austria, South Germany or North Italy.

There are also night trains between Zürich/Munich/Vienna and Venice.

You don’t need a Czech Rail Pass. Just buy a ticket from the border to Prague and from Prague to the border.
The fastest connections Prague to Munich are strangly by two direct local trains. Just buy a ticket in Prague to the Bavarian/Czech border (~ EUR 8,) and when in Bavaria from the German conductor a Bavaria Ticket Single (EUR 19, plus 10% service fee for buying from the conductor). The Bavaria Ticket even covers all local public tranport in Munich itself (U-Bahn, trams, buses). Valid one day.

Use the link to the German rail site at the top of abalada’s post for any train schedule in Europe.

Look at a night train (or maybe a cheap flight) for any trip over about 6 hours. I usually don’t like to take more than about 1 night train a week. You don’t always get much sleep.

I’d seriously look at flying to and from Spain/Portugal — it’s a long way from the rest of the places in your list.