There are direct flights (can be quite cheap) between Venice and Dubrovnik in November but not daily. Personally, I'd try to build my itinerary around taking a direct flight one way or the other, whatever works on the days you happen to be arriving.
Ideally, I would start in Dubrovnik. Either train from Milan directly to Venice and spend a few nights there then fly to Dubrovnik and work your way north...or do it the other way around, if a direct flight works better for you that way. I assume you'll want/need at least the final night in Milan.
So...how many nights do you have total? Fifteen in Europe minus one in Milan? That's fourteen remaining. Let's say three nights in Venice so eleven for everything else.
Here's how I might do it:
Venice (3 nights)
Dubrovnik (2 nights)
Split (3 nights)
Plitvice Lakes National Park (1 night)
Zagreb (2 nights)
Ljubljana/Bled (3 nights)
Milan (1 night)
If the Venice - Dubrovnik flight timing (not every day) works better to fly back to Venice at the end and then train to Milan, then you can do it in reverse.
I added Ljubljana because, first of all, Bled in November might be raining and not much fun, especially without a car and second...Ljubljana is one of my favorite cities in Europe, why isn't it even on your list? ;-) Seriously, in November, I'd rather be based in Ljubljana and do a day trip to Bled, perhaps choosing the day based on the weather. It's easy to get by bus from Ljubljana to Bled; by train is doable if you love trains but less convenient. There is much more going on in Slovenia's capital city at night and museums to see in the day time if it's rainy.
Since it will be a long day to get to Milan at the end, three nights in Slovenia seems prudent.
You could move a night between Dubrovnik and Split based on day trip interests. Dubrovnik itself is small and may be crowded with cruise ship tourists, even in November. Split is more of a "real" city. Figure out what you want to do in each city and decide your itinerary based on that.
I added a night stop in Plitvice Lakes National Park, one of the highlights of Croatia, but I guess you could skip it. I wouldn't.
No, a EURail pass for this region would be a complete waste. You will barely be able to use the trains on my itinerary anyway. There is no rail between Split and Dubrovnik. There is a train between Split and Zagreb, between Zagreb and Ljubljana/Bled, between Slovenia and Italy, but you may wind up taking buses or shuttles instead, anyway. Plan your itinerary first and just buy individual bus, train, or ferry tickets as needed. Both Slovenia and Croatia have good bus systems but limited rail networks. You might catamaran between Split and Dubrovnik, but there is also regular, reliable direct bus service.
You might also consider renting a car in Croatia and maybe even another one in Slovenia. Driving is very easy in these countries and not expensive, generally, especially off season when you are going. A car would make it easier to get between Dubrovnik and Zagreb and allow you to stop in little towns and parks as desired. In Slovenia, you could detour to the town of Skofja Loka between Ljubljana and Bled by car; the scenic drive between Skofja Loka and Bled through the mountains (via Jamnik and Kropa) is spectacular. Maybe just rent a car for the day in Ljubljana. You'd probably want separate cars in Croatia and Slovenia to avoid a steep one-way drop fee.
It's all still doable without a car - by ferry, bus, and sometimes train.
