This may sound odd, but what I did is learn to manual focus. I shoot birds, probably one of the more difficult focussing challenges. Here is how I went about it:
Get a good focus screen. The stock one doesn't show you clearly whether you are in focus or not. I installed an S type from
Focusing Screen
Learn to see focus. It takes practice, but you will notice your ability increase over a couple of months. It will be evidenced by keepers. I find that if I have the time I can reliably manual focus now. It wasn't the case when I started.
Learn to handhold at low shutter speeds. Again another skill that is learnt. Body positioning, using other things to lean on, etc. When the camera doesn't move, the focus mechanism has much less trouble. A monopod or tripod may be required.
Get a good auto focus lens. Some are better than others for the purpose you intend. You will be able to see very clearly when it is in focus and see what it is focussing on. With the ability to hold the camera still and see focus it will be obvious where the focus targets are and you will be able to work with them.
Before I sent my body in for repairs I replaced the original focus screen. They did the work and sent it back, and since I was using a slow 170-500 lens I left the original screen in place. I found that I couldn't see whether I had focus or not. I installed the eeS screen and now I can see. I can work the autofocus mechanism around obstacles, hold focus while recomposing and all that because I can see.
As a final suggestion if you find that you can't get it working to your satisfaction, I would find a way to send the body in for calibration. I'm amazed how much better it is since I got it back. There didn't seem to be any rhyme or reason before, now the body is predictable and accurate.