Hi Bob,
For the most part the images were manually focused. I few were taken using an autofocus 400/5.6 like the last two images in the last set. Stop down metering also but I'm finding it easier to take an incidence reading with my light meter for either f/8 or f/11 and then just dial that in manually. Then I can focus wide open and quickly count clicks as I turn to the right aperture. I actually shot a lot more flying pictures with my 40D and 400/5.6 than the 800/5.6 on the 5D. My main problem was I was using my truck as a blind to shoot from. I had not expected to find the eagles there yet so was not prepared with an adequate way to secure the lens to the truck window area. So I was hesitant to do much action shooting with it yet as I had to pay attention to securing it versus my focusing.
You are correct about some issues with the 5D and adapters. Seems some of the cost cutting decisions with the 5D included tight build tolerances. So a lens/adaptor combo on one 5D may be fine but hit the mirror on another. I have problems with only two of my dozen and a half alternative lenses. My Pentax 50/1.4 will be struck by the mirror anytime it is focused at infinity. My other problem lens is my Contax Ziess 50/1.4 which hits the mirror only when the body is in the vertical position. That is probably some slop in the adapter. Some folks will grind off the bottom of the 5D mirror while others will file down the metal ring on the back of the lens. It is such a rare occurance for me that I still have not selected a solution.