since I have a limited time in Germany, I want to make the most of it
Makes sense to me. The real question here is what constitutes "the most." That's hard to decide without prior experience... so your itinerary depends on your Rick-book in part and on the advice you are asking for here.
For me, "the most" entails not wasting travel time and $CAD on peripheral stuff that really won't improve your understanding of Germany or its people. IMHO you should definitely scuttle those two specific day trips from Munich. In both cases, you already know what you're going to see.
- I like that you have ample time for Berlin. 4 nights might be enough, however. Potsdam might be part of that.
- And I would keep the Rhine as well. It's totally different from Berlin for sure, but at the same time a place that's loaded with a variety of lessons, experiences and choices. IMHO Rick makes an unreasonable fuss over Bacharach. I would focus instead on Cologne (Cathedral, museums,) on Burg Eltz (a detour) and Marksburg (Braubach) castles, a hike on the Rhine Castle Trail and some time meandering some through some old-world wine towns like Oberwesel, Braubach, Boppard (great chairlift ride there) and Limburg (Lahn River,) and yes, 1-2 hours in Bacharach as well. And you probably shouldn't resist taking the Bingen > St. Goar Rhine cruise. I would allocate 3 nights for the area. TIP: Book your nights in Boppard to receive a free train + bus pass for unlimited local train trips throughout your stay.
https://www.boppard-tourismus.de/en/accommodation/
...missing out on Bavaria with the possibility of maybe never ever seeing
it which I think would be a shame.
- You will have time to see see some of Bavaria too...
Rothenburg: Worth seeing, and worth a day trip by train for a visit, but not worth 20% of the nights you have for Germany. NUREMBERG is the ideal Bavarian base town, IMHO, a fantastic city with a dizzying number of choices and great train connections with Berlin and the Rhine. I'd opt for 3 nights here. On one day you can day trip to Rothenburg in about 1.3 hours for a visit of several hours (preferrably on a weekday) very cheaply with VGN Tagesticket Day pass (€23, valid all day long for unlimited journeys within the VGN zone.) If you feel you must visit Munich, you can take a day trip from Nuremberg to Munich and back as well. But Nuremberg itself could easily entertain anyone for 2 days, I think.
The other outstanding Bavarian destination for your trip would be BAMBERG. And fortunately there are direct trains between Nuremberg and Berlin, so you can make a stopover in Bamberg for several hours as you travel between these cities. Bamberg station has lockers for your bags.