The trains we would like to take are Brussels-Cologne-Frankfurt, Frankfurt-Rothenburg- Munich, Munich-Salzburg-Vienna, Vienna-Innsbruck-Bern, Bern-Paris, and finally an overnight from Paris to Rome.
I haven't read through this whole thread, but want to clarify that the only train on your list that requires a seat reservation is Bern-Paris on the TGV Lyria (or Basel-Paris, if you choose a departure that connects there). We advise making that reservation early, since they can sell out, and there are fewer schedules that you might like; you can do it at the same time that you buy the pass. TGV Lyria is the most expensive of all pass holder reservations at about $33 in 2nd class or $68 in first; you can choose 2nd class even with a 1st-class pass. TGV Est reservations from Strasbourg, Colmar, or a German city to Paris are cheaper.
Take the direct ICE from Brussels Nord station to Cologne (or any other connection that doesn't require reservations) to avoid the Thalys seat reservation fee.
[Edit] This is a know issue with the Rail Europe shopping cart that some trains which recommend reservations show up as reservation required. As mentioned above, the German DB site is your accurate resource. I would not bother with the optional German reservations.
A night train also requires a sleeper reservation, but the Paris-Italy night train does not accept rail passes. A separate ticket is the only way. Flying this route is often cheaper; see www.skyscanner.com.
So, you could do this trip with a 5-days-in one month Eurail Global Saver Pass with the current 20% discount at $367 per person in 1st class (or less if you're both under 26). This is very easy to use and flexible for your first 4 travel days.
Or, if you didn't need Switzerland, or if you paid separately from Brussels to the border, the 5-day, 4-country Select Saver Pass costs $334 per person in 1st class.