Zurich-Bernkastel-Kues:
Actually your ticket options are rather easy here - DB Europe Spezial (discounted international ticket) start from 39 euro per person, need to be purchased in advance on DB website -
http://reiseauskunft.bahn.de/bin/query.exe/en?newrequest=yes&protocol=http:& (sales start 90 days before departure). In case of overnight journey timetable the situation with Bernkastel-Kues is slightly more complicated since there is not a lot of overnight trains from Switzerland to Germany, but in our opinion your best choice here is Basel-Kiel overnight IC 2868 (departs Basel 23:26) arrives to Koblenz (closest station on the route to Bernkastel-Kues) at 5:01 to get from Zurich to Basel and from Koblenz to Bernkastel-Kues is quite easy - all the timetables can be found here -
http://reiseauskunft.bahn.de/bin/query.exe/en?newrequest=yes&protocol=http:&Bernkastel-Kues-Rome: Here once again your best option is DB Europr Spezial (tickets start from 43 euro). Best choice in timetable is CNL overnight train from Munich to Rome - you start the journey at app. 2pm and arrive to Rome 9am next morning - all timetables on DB website.
Unfortunately for you in both case there will be couple changes required.
p.s. in case of Bernkastel-Kues-Rome you might also consider flights - 25km from Bernkastel there is big low-cost airlines airport Frankfurt-Hahn (Ryanair operates one-two daily flight to Rome (Ciampino) everyday).