I'm no expert but we did the area around Mindo on our own 2 years ago and can provide some info, for the Amazon, Andes we did an organised tour over 10 years ago then stayed on lodge on Napo River so can give little more than place names or a contact for the tour company.
My round the world trip report from 2019 covers a week in Quito/Mindo
I have spent quite a bit of time in the northern Ecuador area, both East and West slope, including Rio Napo and Mindo. While I am more of a bird photographer than birder, per se, let me know if you would like to discuss our experiences.
Mindo is easy to do, once you get there....but where to go, might be a challenge. My suggestion is to bird the easiest spot in Mind which is in back of Yellow House Hotel/Inn ...etc... Nice group of ladies own the place and they allow you access to their land which extends for miles and hits all the major birds found in the Mindo area. From Mindo, it is a short drive to Milpe Reserve as well as Rio Salanche. The latter is difficult to get to in just a 'car' without four wheel drive. But good birding in all three and doable without a guide for the most part.
Now on the east side, I would start with Guango Lodge just as you start going down the mountain. It rains a lot on this side of the mountains so bring rain boots and gear. From Guango, you can go to several places... San Isidro is perfect and not far away. Wild Sumaco Lodge is perfect too. For those places it is best to have a guide to find the species. You can even hit Gareno Lodge in the Napo if you want something very remote in terms of 'lodgeness' and if you are there, it is easy to hit/bird the Missahuelli area and just stay in town as a base.
In Quito...visit Antisana too (high bird country).
There are others....a few are very expensive so it is up to you but when I was in Ecuador and helped out guiding and taking people around, this is the route I would take. There are also a few more in between Quito and Mindo if you take the back way, but frankly what is in those places can also be found in other places.
You will find quite a bit of overlap in the major species in both the east and west sides.....