Disclaimer - I am not a skilled bird/BIF photographer, so take what I say with a pinch of salt, but here are my thoughts....
For the scenarios you describe, IMHO, there are no easy answers. If your incident light is fluctuating and the reflectivity of your subject and background is also fluctuating, and the size of your subject is variable, then you're going to have to work a bit to get your exposures right. How you approach the problem is partly driven by personal preference and partly by which variable is changing least - the light, the background or the subject.
My approach for the situations you describe would be to set a manual exposure to suit the incident light reaching the subject/scene, probably by spot metering off my palm at +1.3 stops. I would choose a combination of settings which I felt optimised the balance within the exposure triangle - shutter speed not too slow, ISO not too high, aperture optimised for lens IQ without jeopardising the other values. What those optimum values are depends on many things - camera body, lens, light levels, subject activity level, photographer skills, camera/lens stability, need to crop, enlargement/reproduction size, amount of fine detail content, tolerance to accept noise or need to suppress it.
In bright light (yes, Sunny 16) the optimum combination for a 1D3 and 100-400 might be something like 1/1600, f/8, 400 ISO. That would be a pretty decent combination for low shake/blur, high lens IQ and low noise. As the light levels drop you need to chip away at each in turn, until you end up at something like 1/800, f/5.6, 1600 ISO, which is 4 stops dimmer than "Sunny 16" and my threshold for giving up on shooting BIF, since I have a 100-400. With a faster, sharper lens I see no reason not to shoot at f/4 if you have it available. If you can fill the frame then even shooting at 3200 ISO is not out of the question, but very high ISO, small subjects and fine feather details are not a good combination, so I'd say only go that route if you can avoid cropping.
With my optimum settings dialed in, whatever they might be for the circumstances at the moment, I would simply remain aware of fluctuating light levels and adjust as necessary, or wait until my preferred lighting returned. Choosing which exposure control to adjust as the light changed would depend on exactly which values I had set currently, and which adjustment would most improve IQ or least harm it. I would already have figured out in my mind which exposure variables to adjust, depending on which way the light altered.
It is easy enough to remeter and adjust settings within five seconds. If the light is changing faster than that then I guess you are in trouble. Otherwise, simply keep on top of the light as it changes and be ready to shoot in advance, before your subject makes an appearance or does its thing. If I'm on walkabout I will periodically check my metering and exposure, just as I walk along. That way, as soon as anything interesting appears I am ready to shoot. If the light is up and down like a whore's drawers then I'll choose which lighting condition I would prefer to shoot in (probably the brighter conditions) and set the camera up for that light level. If an opportunity presents itself when the light is "wrong" for my settings then I'll just have to deal with it as best I can or miss the shot.
Overall I find the benefits of my approach to outweigh the cons, so I stick with it. I have pretty much entirely given up on autoexposure, so if you want an answer that takes that approach I'm afraid you'll need to look to someone else for their thoughts on the matter.
As for IS settings, I'm still experimenting. If the shutter speed is high enough (1/1600+) then it's probably best turned off. At 1/800 and slower I feel it is best turned on, but it is important to pick the right mode for the movement of the subject. If your subject is soaring and swooping and flitting about then turn it off. If it is moving steadily towards you (no jerky camera movements to track it) then Mode 1 would be best. If you need to pan, either up or down, but not diagonally, then Mode 2 is the right choice. A combination pan (diagonal) does not play well with IS, unless your panning is slow, controlled and steady. Trying to pan a dive or a bird landing is probably best tackled with IS off.
I don't know if that is any help, but it's the best I can do.