Updated Itinerary Help Requested

Is this trip still September? And how many days? Four travelers?
Initially I'd say into Venice and out of Milan. You are referring to Menaggio, Lake Como, right? It's an hour regional train to Milan from Varenna, Lake Como.
I just read your earlier posts, and appreciate your struggle with the decisions to revise the itinerary, skipping Rome. Glad you are still going.
Use Google Flights to research airlines and routes, and set up Flight Alerts to track prices.
Download the two Italy train companies' apps and work out routes that involved fewer train changes and shorter length of travel. It will help to print out maps on which you can sketch out routes , or use Google maps to visualize the routes.
You will get there and have a wonderful trip! Safe travels!

Mid September-early October.

Easier to fly IN to Venice than out of and it’s the perfect place to get over jet lag

Venice
Bologna area
CT
Florence
Mennagio
Fly out of Milan - you’ll need to stay in or near Milan night before departure

I haven't traveled this route, but try inputting -
Venice
Bologna
Florence
CT
Lake Como
Milan (fly)
Into Google Maps

However, there are many folks here who are a lot more skillful than I am with map management.
Good luck!

I concur with Christine's suggestion, but would advise to be in Milan ( or by airport), , not just near Milan the last night.

Our 1st trip to Italy had us flying home from Milan and the flight left early. ( before 9AM )
We stayed at a hotel near the airport that had shuttle service. Made for a stress free departure vs an " o'dark ugly" wake up in Milan to get a train/bus to the airport.

Recommend flying in and out of Milan as there are more selection of flights from there. Recommend staying in LaSpezia to see Cinque Terre. Then travel to Florence, stopping in Pisa on the way to Florence (story you luggage at the train station). From Florence take day trips (we went to Siena and Bologna). Then take the train to Venice. From Venice travel to Verona. End your trip in Milan. While in Milan you can take day trips too such as Lake Como.

I'll echo the recommendation for La Spezia as headquarters for visiting the Cinque Terre, especially for those who love good food. The old town in La Spezia was one of our favorite places in Italy, and visiting the marina with its many superyachts was great fun.