Trains from Munich to Florence

I have no comments on the itinerary.
RailEurope and Trainline are reputable, as is Loco2.com, which is my current favorite for ease of use and lack of fees. I prefer to use companies that provide print at home tickets, too.

Loco2 does the journey for € 39,90 (Munich to Bologna) plus € 16,90 (Bologna to Florence) for a random date early September.
I don't know how it works with Trainline and RailEurope, but Loco2 allows for choosing a later train for the Bologna-Florence leg, giving you the peace of mind of not missing that connection.
Bahn.de is the best choice for trains run by the company. In this case Bologna to Florence is done by Trenitalia, which is possibly also the reason they can't send you the tickets as an email attachment for printing at home.

Added:
Alternative is to buy your tickets separately with the Bahn (Munich-Bologna) and Trenitalia (Bologna-Florence).

RailEurope can be linked through this Rick Steves website, so its legit. As a third party re-seller of tickets, there's an added cost to their tickets. Some people don't like them because they don't always show all available trains and routes. Just make sure you are comparing the exact same tickets and trains when you look at prices.

Just a thought, but have you considered flying?
I see direct flights in September for less than USD$50 one-way ... taking about an hour and 10 minutes versus the 8 hours (or more) it would take to do the same journey by train.
Even with the usual hassles of getting to and from the airports you'd still be saving most of a day.

I'm going to echo Robert's suggestion of flying. I love European train rides, but yours is a very long one. Flying is so much easier. Getting to the Munich airport is easy on the Sbahn, and it's a short ride on the new shuttle from the Florence airport to the SMN station. (Or a fairly inexpensive taxi straight to your hotel).

The Florence airport shuttle CJean refers to is the T2 tram. It's still just 1.50 euro per person and takes only around 20 minutes to reach SMN.

The incoming train will likely arrive at the surface tracks in Bologna, while the train to Florence leaves from the underground tracks. 12 minutes is definitely too short a time.

I am with Robert and cjean wondering why you are not flying (or considering it)

Fastest train looks to be 7hr 35 min and one change

Depending on the composition of the group, making a short connection time may be unwise. Getting a schedule that provides a longer connection time makes the trip 8+ hrs.
As you are flying within the Schengen area, a flight would be as simple as a Vancouver to Calgary flight

Flight is 1 hr 10 min

Depending when you are traveling, the fare difference may not be meaningful.

Another way would be to take the Flixbus, direct from Munich to Florence.
There are 4 direct buses to Florence villa Constanza, and from there you have a direct tramway to Santa Maria Novella.
If you travel during the night, you might also sève a hotel night.

Price is between 30-50 euros