hey hey jen
as others have mentioned, know number of nights in the places you want. september/october was a time people traveled, but now days it doesn't seem to matter, it's busy. it's harvest/festival time, conferences/conventions, people wanting to see the same places you are looking at, some activities/attractions need to be booked ahead of time and some are reserving day/times.
many morning flights into venice, checkin times usually 2-4pm, what you do with luggage (do they offer a hold until that time, not lugging around stairs/steps, crossing bridges, uneven pavement, jet lag is real day 2 you may be tired you may not, how much you hoping to see and do, day 3 is check out by 10-11am
europeforvisitors.com and seat61.com
so much info about traveling in italy and on trains.
will you be renting a car at all? hope, it's not useful with cost of parking, tolls, ZTL zones with high fines. trains are usually city center to city center, taxis are available, no hailing from street, pick up at taxi stop, always validate your train ticket before boarding train at little metal box at train track, pack light, no fun with heavy bags, we have sink washed clothes, hang to dry (i bring a small container of detergent)
same thing for traveling to the rest of your cities. backtracking, spending more time on trains, is not "relaxing" to me. i would go straight to lake como from venice, no stopping to spend night in milan, and have extra day on the lake.
balso makes a comment about milan being an enjoyable city to visit and roam around for couple days. but many here use it as a dropping off/picking up transportation at train station.
where in cinque terre? take the train from lake como straight to cinque terre and relax evening night time. then onto florence, and where in tuscany knowing florence is part of tuscany? a big area to chose where you want stay.
"tuscany" first then back to florence for your days then onto rome.
have a great map, mark your spots/areas you want to see/do, times of trains arriving and departing, lots to think about as first timers to italy. with research, asking questions to get good bad and ugly, you will be happy with what you've accomplished. just here to help you out, this forum is great. have a great time
aloha