Travel Plan

Hi Chris! Well, that's a tough question to answer since it all depends upon what you want to see/do in those cities. On first glance, it seems you will be covering a lot of territory in a relatively short period of time - even traveling in the evening by train it doesn't give you a lot of "down time" nor a whole lot of wiggle room for delayed trains, getting lost/oriented, finding your accomodation, checking in/checking out, etc. If you travel very light and sleep well on trains, it may work fine for you! I travel light but I don't sleep well on trains so the Munich/ Venice piece wouldn't work for me - after 9 1/2 hours on a train (even at night) I'd be pretty worthless the next day!
Perhaps if you provided a bit more detail about what you want to see in those cities and your "mode" of travel, we can be a bit more helpful!!

Chris, are you including travel days, I mean for instance, if you count 4 days in Paris to include your arrival and departure days,then you really only have 2 whole days there, so in my case when I do my plan I don't count travel days as sightseeing days, ( although you can often get a bit done later in the day, keeping in mind some museums and monuments etc close by 5 or 530 sometimes)
Personally ( and yes, its all about ones own preferences ultimately) I would drop a few places on your list so I could really enjoy seeing more at some other places, but thats just me, I think Rome, Paris, need at least 4 full days there to see even a portion of sites.

when is this trip?

Hi, Yes. From your schedule I suggest the Amsterdam-Berlin night train and also by night Munich-Venice (includes a transfer in Verona). Berlin-Munich isn't really worth a night train unless you continue on to Vienna, which I've done. But there is a direct connection on ICE for Berlin-Munich...you want to arrive in Munich by 1430. The two night train rides get you into Berlin Hbf and Venice early enough in the morning to give a whole day. There's hotel/hostel two mins away from Berlin Hbf....Meininger Hotel. At Munich Hbf there are number of small hotels, Pensionen, such as those on Schillerstrasse, and three hostels not more than 5 mins from the Hbf. This is the immediate area I stay in Munich.

Use the search engine skyscanner.com to see all your airline choices, both budget airlines and national carriers. For Madrid-Paris you could either take a direct night train or fly on a budget airline. There is a direct night train from Amsterdam to Berlin, but it arrives at 04:26. Daytime routes take 6-7 hours. The night train from Munich to Venice goes there directly. No connection in Verona. Eurail is a travel agency, not a railroad. You will be traveling on trains operated by each country's national rail company. Exception: Thalys trains from Paris to Amsterdam are owned by a consortium. Even if you won't spend a whole day doing it, for the sake of planning add one day for travel between each city. When are you taking this trip? You can get discount fares for many of your train rides if you book well in advance (usually up to 90 days allowed).

Chris, Day or night there is one direct Munich-Venice connection. As pointed out above, the CNL train is direct...sorry about that, and all the better. The other day routes do include a transfer in Verona. I myself would take the CNL for both Berlin and Venice.