In general, what I shoot (angling) doesn't really require fast shutters other than when doing casting shots but to be on the safe side, especially when it comes to having maximum DoF at any given situation, I usually look for a worse case exposure setting that is then my base for the day. I know the capabilities of my camera and up to ISO 1000 it's fine so more often than not, I'll set it at a higher ISO so I get fast shutters and narrow apertures. This then means I have a lot of leeway to play with and if light levels improve, I can drop the ISO down.
The only thing I do have to be mindful of is FP sync and the loss of power than comes with trying to sync faster than 1/250th, where it can be as much as three stops of flash power lost as a result. that's the only time I start to look at shutter speeds and in that scenario, I drop the ISO right down because i usually want shallow DoF as well. Of course, for bird stuff i doubt flash is going to be that much of a problem for you.....
What you're suggesting about using Auto ISO (but setting a high ISO 'ceiling') sounds a good plan. I'd just do what I normally do; look at how bad the light could get and what shutter speed/aperture combo you'll need to freeze action AND get a good DoF and then you can work from there. I've had a look at a few samples of D5000 high ISO and TBH, I actually wouldn't mind pushing it to ISO 1600 if I were you... if it means getting a shot that's not going to happen at lower ISOs then personally, I'd suffer a bit of extra noise.