Difficult to get a great picture in this situation, the bird was never clear from branches and things. Flash is out of the question for me since I'm dedicated to natural light.
In this very situation to get a good quality picture I would need a fstop more light and the bird to stay in a good position for about 20 seconds. Since he was a little bit far away (and high up) I would keep the extender on but switch to ISO800, use live view and with some luck I could get a decent one. If the bird was closer the extender will go off of course. With more careful post processing I can get rid of the noise. All in all I'm quite happy with these pictures, just seeing this bird is a privilege.
It's difficult to have a best setup ready for any possible situation. However I have the extender off normally with the 50D (but on with the 40D).