That sounds like your trying to make me break my Mamiya 500mm f/4.5 with that manual focusing talk.
I guess that's a pick-your-poison thing
Thoughts on shutter speed? I want to bring my ambient light up and bring down my my ISO, I decided to first rent the 400mm f/2.8 so if I shoot it at 2.8 I might be able to achieve this.
Depends a lot on what ambient light you're working with. In the two photos above I set the feeder up so that it would be at the edge of shade at the day's first light with the dawn sky behind me; shutter speed was 1/500 sec, ISO 400, f/4. The photo below was in full sunlight, ISO 400, 1/3000 sec @ f/8
I don't know that a 400mm f/2.8 is going to help much. I found that the huge entrance pupil of the 400mm f/2.8 (mine was a Canon, emphasis on
was) freaked the critters out where a slower lens didn't. I had to use extenders on the 400/2.8 nearly all the time because I couldn't get close enough. Slower lens like a 400mm f/5.6, not nearly as much of a problem. With the 400/2.8 DOF wide open at close range was minuscule too, like "which part of the eyeball do you want in focus" minuscule.
Likewise I don't think the flash will help much. One pop and "my" birds were gone. It sounds to me like you're trying to solve the problem with technology where technique can work as well if not better (and certainly more economically).