If I've got my sums right the D5000 pixels are each about 30 µm² in area. That's handy when looking at the interactive chart on the CambridgeInColour Diffraction Limited Photography
page as it's the same as the Nikon D2X. Put the mouse over the "Nikon D2X" text in the chart and then move it sideways to the left until it's in the Aperture column. You can now move it up and down and see how diffraction is affected by f-number. As you can see f/11 is about right though you could probably get away with f/16 if you needed extreme DoF.
Manual focus is a good technique if you are trying to focus at the hyperfocal distance to maximise DoF. I'm a bit lazier so if I can find an element of the scene at the right distance which won't also mess up the exposure I point my camera at that, press the shutter button halfway to let AF and autoexposure do their things and then recompose.
It's not possible to tell from the shot above if everything is in focus. To do that we'd have to see one or more 100% crops from areas of concern. On a post-processing note, bear in mind that when reducing the size of an image the loss in resolution means that for fine detailed subjects it sometimes helps if you add a little extra sharpening to compensate.