Acknowledging you have a disabled adult.
1: I probably wouldn't stay downtown. You could catch a Rockies game if in town - great experience. You could check out Meow Wolf. Then get a hotel further south like the Tech Center
2: Garden of the Gods is cool and free. Pikes Peak Cog is kind of a rip off. You could drive up if you want. The Cheyenne Mountain Zoo in CO Springs is really really good (not just for kids). You could also walk around The Broadmoor or do a few other things.
3: You can't drive across Royal Gorge Bridge - pedestrian only. There's some stuff to do there. Likely not going to raft that time of year. Skyline drive is a road on a ridge that is a little adventurous. You could go to Bishop Castle
4: Sand Dunes are great. Rent a sand board/sled at the local sports shop in Alamosa to slide down some dunes. Fun time. There is a gator farm just north of Alamosa that's really interesting and enjoyable (hot springs = Tilapia = carcasses = need something to rid themselves of it = gators)
5: Have only driven through Pagosa Springs, but I want to go and the hot springs are the main attraction. I think there are free spots in the river that are hot if you do a little research. Otherwise, you can pay for the developed part
6: You can do the train. It's good and beautiful, but you'd have to return to Durango and then drive the same way. Depends on what you want to do, but Durango is lovely. Silverton is a smaller old mining town with one paved road and a normal strip of restaurants and stores.
7: YES to the million dollar highway (not as scary as some make it out to be). Just stunning. Make stops along the way. Great views. We saw a moose. In Ouray, they have via ferratas, but maybe with your age and daughter, not something to do. You can do parts of the perimeter trail (like short hike/walk to Cascade Falls). The Hot Springs there are more like a rec pool
8: Black Canyon of the Gunnison is underrated. Agree with the 'drive, short walks to viewpoints' that you can do there.
9: Along the way from Montrose to Aspen, you could do CO National Monument (drive, some short hikes/views) and/or Glenwood Springs (hot springs just expanded, there is an amusement park at the top y'all might like). Short walk to view Maroon Bells in Aspen is beautiful.
10: As mentioned, get an entry time. Shouldn't be too hard that time of year, but good to do ahead (can't remember how many days before it opens up). Stop at the top of course. Also see if you can get an entry time to Bear Lake area. There is a paved walk around that like or a more moderately difficult hike up to Emerald lake (stunning!). Look for Mountain Goats up high. Estes Park is a nice town - a lot of road construction going on in the middle of town. If you are there in late Sep, it is likely Elk rut season, so they will be all over town. Be careful (and book hotel ASAP).
11: Sounds like this would be getting out of the mountains back to Denver. You could stop at Bucees on I-25 near Johnson Corner.

Good luck and sounds like an amazing trip