I've, classically, shot the 100-400 MkI around 1/640 to 1/1250, f/5.6 and whatever ISO necessary to maintain those. Occasionally dipping down just under 1/400. Anything up to ISO 3200 should be just fine for you, as long as you expose slightly to the right and pull things down in post rather than pushing up your shadows.
If you're noticing front focus issues at 400mm, I would certainly MFA that puppy. I had to MFA my MkI on all of my bodies (that support it) to get the best performance out of it anyway.
As far as AF goes, you need to be close enough that the subject fills at least your primary AF point; if you're any farther away you're going to get wildly differing results, as there isn't enough of your subject there for the camera to focus on, reliably, or to be recorded by a reasonable number of pixels. I have a number of heavy crops, but virtually none of them from so far out that the subject was encircled by the primary AF point.
Especially with birds, you are going to find that you do need to crop fairly often, even at 400mm on a crop sensor; at least, I do. It's just a fact of life shooting these subjects at these focal lengths.
The sample images you supplied though look like you're doing alright.
This was, easily, my absolute worst-case shooting situation while I was up there in 2013. We were on a harbor cruise out of Seward, on a tour boat in a rolling bay, heavy gray conditions with rain...so dark and moving.
Any better conditions and you should be just fine.