Kombi:

At 1/2000 sec exposure time, you have room to bring that down and close your apeture to give more DOF. With a flash you can close your apeture even more for more DOF.

Also, with hand holding, the macro DOF tends to be so narrow that if you prefocus and delay taking the shot (or focus and recompose), then you are not likely be able to hold your focal plane where you intended. Any sway in your body or head will be moving the focus forward/back of your focal point. Macro is really made for tripods, but if you hand hold, then push the shutter button all the way down so the shot is taken as soon as focus is achieved - this reduces the chance that your body movement will move your focus point.

What I have found most effective is as "andnowimbroke" stated. Use live view on a tripod, blow it up 10x and AF or manually focus, then use a remote shutter release. I had to put in a +16 AFMA on my lens to get it to focus properly... so if your AF is not focusing where you think it should, then manually focus.