D90 Focus Problem? Please help!

I upgraded from a D50 to a D90 nearly a year ago (lens mount on D50 broke) and have been frustrated and downright depressed with the sharpness of my shots from this new camera. Sweet memories of my young children are slipping by uncaptured because I don't even want to pull the camera out of the bag anymore.

I'm a TOTAL newby on this, so please go easy on me. I've never included photos in a post, and I've only ever posted one or two times, so I don't know if I'm even going about this in the correct way.

I've spent countless hours over the last few days taking shot after shot trying to determine if it's operator error, a problem with my equipment, or unrealistic expectations. I've tested with both a Nikon 50mm 1.4 AF lens and a Nikon 24-70mm 2.8 lens with similar results. The photos below are with the 50mm because it should presumably be sharper and I was hopeful that the narrow DOF would help isolate the problem.

Here are two of the test photos and the specs common to both photos:

D90, Nikon 50mm 1.4 AF lens (no filter), f1.4, iso 200, af-s, single-point af area.

Test #1 carried out per the instructions here ( http://www.focustestchart.com/chart.html ):

Photo-specific Info:

1/4000 shutter speed, subject distance .5 meters, taken on a tripod using the self-timer to try and rule out camera shake.

To me, the wording "This text should be perfectly in focus" is not focused.

Test #2:

Photo Info:

1/80 shutter speed, subject distance 1 meter, handheld (no tripod or self-timer used).

To me, the wood on the bed is more focused than the eyes. Why the heck can't I ever seem to get my kids' eyes sharply focused when that's exactly where I am placing the camera's focal point indicator? I used to be a focus/recomposer but have now tried to retrain myself to compose and then move the focal point using the arrow keys on the back of the camera.

Thoughts? What else should I try? I'm at my wit's end on this thing and would be forever grateful to anyone who could help me.