@Kassie;
You've gotten some pretty good advice so far..and, your shots are not bad.
I think that one of the key areas here, it has been mentioned several times, is to use a faster shutter speed.  One way to do that is to increase the ISO speed (yes, it comes with a sacrifice of image noise)...but bumping it up will allow you to use a bit faster shutter speed that may be the cause of the soft images.
Another few points to consider;

1. When you manually focus....are you sure that the focus is correct?...the reason I ask is that the viewfinder screens on most DSLR's are not ideally set up for manual focusing (split screen)...perhaps check the diopter adjustment if necessary...
2. Out of the cam images generally require some measure of sharpening in post process...though, I do not think it would help terribly much here.

I would also heed danob's advice and practice with just the 400mm alone ( without the tele extender)....get comfortable with that first.  Wildlife telephotography, like high magnification macro work requires a fair bit of practice to understand the limitations of both the equipment and the photographer.

With time, I am sure things wil fall into place and your  images will come out the way you expect.

Good Luck.

In youth, we learn....with age, we understand.