Bavarian itinerary

I do not see the value to spend more than one night in Rothenburg - if you want to do this detour.

My wife and I both enjoy the outdoors and the older/ Bavarian architecture

"older/ Bavarian architecture": what is older? what is Bavarian?
Maybe have a look at two parts of German Half-Timbered House Road.

For "outdoors" I recommend more time in southern Black Wood Forest - north of Freiburg.

Seems that Zurich saves money but wastes time - what do you have more of?

What is your planned mean of transport?

2 weeks: a nice amount of time.

September 4th- 6th stay in Freiburg

Not clear to me what this is about. Do you plan to pick up a car there? If you are heading to Rothenburg or some other place in Bavaria afterward, as you seem to be, I think it might be wiser to avoid this heavy detour to the west. Have a look at Konstanz, NE of Zurich on pretty Lake Constance, for your first night. It's only about 90 minutes by train from ZRH airport. You can get a car there in all likelihood. Radolfzell, Meersburg and Lindau (which is actually in Bavaria) are very attractive and worthwhile destinations. Maybe Insel Mainau would also be interesting for you. From Lindau it's a fairly short drive over to the Romantic Road.

https://www.tripadvisor.com/Attraction_Review-g198393-d498416-Reviews-Isle_of_Mainau-Konstanz_Baden_Wurttemberg.html

September 6th-8th- Stay in Rothenburg

As MarkK says, one night is plenty. It's a small town. But nearby are some other gems that you should look into. This area of Bavaria is known as FRANCONIA, which has its own special flavor. Be sure to visit Bad Windsheim, very near Rothenburg, if you are serious about seeing local architecture over the last 700 years; this place is eye-opening, with traditional Franconian food in the onsite restaurants and its own brewery to boot:

https://www.tripadvisor.com/Attraction_Review-g198421-d284746-Reviews-Frankonian_Open_Air_Museum-Bad_Windsheim_Middle_Franconia_Franconia_Bavaria.html

https://www.youtube.com/watch?v=WqCUq_5o-FA

Sommerhausen, a Franconian town on the Main River near the Romantic Road town of Würzburg, is also a gem:

https://www.youtube.com/watch?v=0AeGts3FIZA&t=10s

Ochsenfurt and Marktbreit are neighboring riverside towns to Sommerhausen. All three towns are part of the Half-timbered House route which MarkK mentions and have some lovely old-world architecture, the kind you will not find in southern Bavaria. See map linking Half-timbered House route towns:

https://www.deutsche-fachwerkstrasse.de/Regionalstrecken_Staedte/Franken.html

STRONG RECOMMENDATION FOR HOTEL CHRISTINE IN FUSSEN!!!

We just spent a few days there. The hotelier/chef and his small staff are FANTASTIC!

He makes a wonderful breakfast -- unlike the buffet you'll find in most hotels. Staff serves it up. He was evidently a Michelin 1-star chef. He runs the friendliest place. Great appointments. And it's walking distance to the old Town but away from the noise.

Our room with a balcony looked at the castle.

As I say STRONG RECOMMENDATION!

I spent 4 nights in Rothenburg last fall - my 5th visit. I see nothing wrong spending 2 nights there

I had picked Rothenburg earlier in the initial outline and now I’m having second thoughts.

Both Freiburg im Breisgau and Rothenberg seem out of the way for the circuit you're planning, so eliminating one of those might make sense. Getting rid of Rothenberg alone saves you 300 km of travel, fwiw. Freiberg to Fussen though is a 4 hour drive.

We have visited all the places that you mentioned and enjoyed them. Freiburg and Rothenburg were favorites on trips in the last couple of years. Your lengths of stay seem reasonable to me.

It appears that you have checked the driving times between destinations. We were stationed in Germany with our own car. We had to be careful not to give away too much vacation time to riding about in the car. You mentioned liking outdoors. Sightseeing on foot is best for us, maybe for you as well. BTW, Rothenburg is one of our favorite places to get outside the town walls and take a walk in the country: either down to Detwang or through the vineyards.

Agree with Stephen and Gary Mc, we loved our two night stay in Rothenburg. And yes to getting outside the walls, beautiful countryside, go see the Topper house inside.

Freiburg is a nice town. I spent quite a bit of time there.

But I would never recommend it as a destination unless it was a stopover on the way to Alsace