since you are going by train you may want to look at www.bahn.de - the German Railways web site for pricing and if you want to lock yourself into a non-changeble non-refundable ticket weeks ahead of time (talking about the SPAR type fares - deep discounted ticket which are sold in limited numbers and can sell out long before the train - that may be the cheapest way to go.

But if you want flexibility to just hop any train anytime then investigate the German Railpass which allows exactly that and if compared to regular hop on fares the pass, since you are doing some long-distance trains, may well be cheaper and give you the ability to just show up at stations and hop on any of the zillions of daily train. Passes similar allow you to hop on K-D boats on The Rhine - 100% coverage of fares - just flash pass when boarding.

for oodles of great info on German trains I always spotlight these IMO Uber fantastic sites - http://www.budgeteuropetravel.com/id9.html; www.ricksteves.com and www.seat61.com - the latter has good info on the SPAR typo discount fares at www.bahn.de.

I would do Cologne as a day trip from your Rhine base - one less relocation, always a hassle and Cologne IMO after being there zillions of times is one of the least romantic cities in Germany - or make it a few-hour stop when coming from Berlin - put bags in train station locker next door to fantastic cathedral and then move onto Bacharach.

do not neglect the Mosel Valley as many find it prettier than the Rhine and it also has castles, including Burg Eltz, one of the most famous castles in Germany and unlike most in the area that are ruined still in its pristine medieval condition.

It is doable. It is probably between makes sense and too aggressive. It is in the details and which trains (departure times) you are taking. How do you get 3 days in Berlin with only 2 nights? It might make sense to skip the night in Cologne and adding a night to either Berlin or Bacharach.Are you staying 2 nights in Rothenburg? Below is a link to the Romantic Road bus from Rothenburg to Munich.

http://www.touring-travel.eu/index.php?id=6&L=2&tttlng=2

"Any help on if this makes sense / too aggressive / what the heck are you thinking would be greatly appreciated.
9/15- 9/17 Berlin - stay 2 nights 3 days (do all the sites)
9/17 - 9/18 Train to Cologne stay 1 night
9/18 -9/20 train to Koblenz / Bacharach stay in Bacharach - Tour the castles
9/20 - 9/21 Train to Rothenberg ob der Tauber find a tour"

You don't have adequate time in Berlin. Spend 3 nights.

I don't think Cologne is worth an overnight, given your time constraints. I would simply stop there enroute to Bacharach instead - and add the night you save to Berlin. Use lockers to stow your bags there, see the Cathedral or whatever you have in mind, and proceed to Bacharach afterward. At the DB site, I see fares of 69 and 79€ on Sept. 18 for a one-way ticket for Berlin-Bacharach with a 3.5-hour stopover in Cologne. Leave at 8:50, arrive 18:30 in Bacharach. (Of course you can use a railpass day if you're getting one of those.)

Also, to save time, I suggest you stay in St. Goar instead of Bacharach - it's a better base for train travelers in the area, Rheinfels Castle is right there, there's a ferry that will get you over to the east bank to see the best castle in the area - Marksburg - and in St. Goar the scenery is better than Bacharach - it's maybe the prettiest part of the river, and you can see 3 castles from the riverfront.

I wouldn't bother with that Romantic Road bus. The RR isn't all that scenic or romantic, really, and the bus gives you next to no time at all in the towns it passes through.

I suggest that on the way to R'burg, you make a stop for a few hours (like you did in Cologne) in Würzburg, one of the RR towns, which is home to one of Germany's more amazing palaces - the Residenz.

I agree that I would drop Cologne from the plan. You will find your time spent better elsewhere.

Are you traveling alone? What is your age. How long is your stay in Munich?

Oktoberfest is famous and it is good to experience it at least once. You will want reservations in one of the Beer tents if you can get it for this Bavarian version of a kegger.

Rothenburg is a favorite destination for bus tours, wheter Grayline or Big Bus tours by escourted tour companies. You might contact Grayline in Munich about hooking up with one of their busses coming back to Munich from a daytrip to Rothenburg.