Would this be doable in 12 days: (any suggestions?)

Day 1- Munich
Day 2- Train to Bolzano, Italy
Day 3- Train to Florence, Italy
Day 6- Bus to Siena
Day 10- Back to northern Italy-- via train- Any suggestions for good northern italian cities/towns to visit or stop in Innsbruck?
Day 12- Munich

Yes very well paced - I'd add a day to Munich - if landing there and taking off on days 1 and 12 you have little time for Munich - great base for day trips - like to Salzburg, Austria - about an hour and a half by train or to Fussen for Mad Ludwig's Neuschwanstein Castle or to the suburbs and Dachau or to Nurnberg if interested in Third Reich relics - the most of any city and on and on - might be more ejoyable than anhy town in northern Italy though Verona is a very historic and lovely city - hard to beat - maybe substitute it for Bolzano?

Here are some sights to check on rail travel ins and outs: www.seat61.com - great info on discounted tickets for all those trains if you want to book in stone weeks in advance to get those limited in number ducats; www.budgeteuropetravel.com and www.ricksteves.com - you are not traveling nearly enough on trains to consider any railpass and IME first class is a much more releaxed ride - esp for those with typically 'too much' luggage - discounted tickets also come in first class - but early bird gets the discounted worm so if OK with booking in stone weeks ahead as many are save money by doing so over walk up fares but they are in practice non-changeable non-refundable.

Personally I would rather spend time in the Dolomiti than Siena, but that is not the way everybody feels. If you are going during a time of year when you can't enjoy the Dolomiti due to the likelihood of poor weather and visibility, I would suggest simply going from Munich to Verona, and skipping Bolzano.

On your return, consider stopping in Trento or Bressanone (Brixen).

Yup Verona trumps Bolzano or Trento - nice and Germanic as they may be - Verona is exceptional for a day or even two. Could also do a day on nearby Lake Garda or even base there if want to do what to me is Italy's loveliest and most interesting lake. Two towns at the southern end of the lake are railheads for it. Change at Verona to regional trains.