First trip to Italy! And Switzerland.....

Personally, I might start in Rome and head north to Switzerland via Venice - unless you have found a direct flight from Rome to Murren? Otherwise, you'll have a long train trip backtrack to Switzerland from Rome. The train ride from Milan to Rome is about the same duration as - just a tad longer than - the ride from Milan to Venice. If you want to do Florence, you could start there, too, then do Rome, then back up to Venice and then up to Switzerland.

(I assume it's too late to fly into Rome instead - which would save a few hours' travel one way when you have to backtrack, of course.)

There is no "expert" opinion for how many nights to stay in one town or another. Even seasoned travelers have vastly different travel preferences. Some of us prefer to travel at a faster clip than others. I would have no trouble spending a few nights in Florence on the itinerary you have planned.

I'm also not someone who needs a lot of time "recovering" from jet lag. I tend to hit the ground running and stay awake all day the first day, even though I haven't slept on the long transatlantic flight. (Some people can sleep on a plane - I envy them!) Yes, that first day I'm pretty tired but I see no point in wasting it recovering. I'm fine by day two after a good night's sleep the first night.
Some people do plan some "recovery time" for jet lag into their schedule, though. Up to you.

Look into flights (some airlines are cheaper than the trains for this distance) from Rome to Zurich or Bern. Then take the train from there to Murren. That will save you a lot of time, plus should be less expensive.

If you look on the map (rome2rio.com) for your train from Murren back into the Milan area; you're coming right along Lake Maggiore. We stayed at Stresa two nights when we left Wengen, Switzerland, and it's a beautiful lake. You can take the ferry out to explore Isola Bella (beautiful gardens & villa) and Isola Pescatori for lunch. Stresa is close enough to the Milan airport that you can arrange a shuttle.

If you are committed on our flights being into/out of Milan here is a suggestion

Lake Como to Venice to Rome to Florence to Milan

Varenna is easy from Milan Centrale, so going there on arrival day would be in my mind a great way to start your vacation.

CT is an out of the way locale for your limited time. You could swap it for Lake Como, but going to both in a 2 week trip is probably too much travel time.

If you can adjust your flights, go into Milan and out of Rome or vice versa. One way travel is best use of time.

To me, trying to do Rome and Murren on a 2 week trip is more train time than I would want to do.

If you do choose to do your "plan B" I would add days in Venice and Rome and keep it to 3 destinations

that's my 2 copper Lincolns

Logistically, kind of all over the place. And there's no easy, efficient way to get to Murren, but it's supposedly one of the more beautiful places on the planet.

Here's what I'd do, trying unsuccessfully to avoid extra flights because I love European trains and they are part of the experience, but at the same time trying to limit hours per day on the train, because too long and they aren't so fun anymore. Numbers are nights on the ground:

Arrive Milan
(train to Rome [3 hrs])
Rome 5
(train Rome/Venice [3 hr 45 min])
Venice 3
(fly Venice/Zurich [nonstop 1 hr 15 min])
Zurich 0-1 (air/train schedules may allow you to not have to stay in Zurich, go right on to Murren)
(train Zurich/Murren [3 hr 20 min])
Murren 4-5
(train to Milan [4 hr 30 min])
Milan 1
Depart Milan

Enjoy your planning!