My idea was at least 3 separate trips, one for the East and West slopes, one for the South, and one for Amazon and Galapagos. I know I won't see all of the species like that, but at least get me upwards of 700 species which is not too bad after 6 weeks in a country as rich as Ecuador.
I would probably do this differently. First trip to Ecuador NW slope up to the top but at the most to Guango on the east slope. Then I would do max one week on the lower parts of east slope and the rest in Amazon, third trip to the south and a fourth trip to combine Galapagos with cleaning up some other spots for things you still need. What is important to realize, is that Galapagos gives you low species number but high value on the experience scale. Another thing to notice is that a standard tour around Galapagos gives you access to about half the endemics, you need two different tours or one specialized bird tour to get most. You need to add independent island hopping to get the last one or two.