Well you insteinctivly went about it the right way, for macro photography Manual focus is really the only way to do it. Often times AF either gets lost searching and gives up or finds the wrong target.
As for your lighting. I know the feeling of improvised lighting, I do it all the time. With macro this becomes difficult as generally more light is needed for macro shooting especially if handheld. A good multifunction answer to this is a Maglight flashlight. I use one all the time.
Here is a super macro taken with nothing more than a desk lamp and a maglight.
Now....with your DOF, this is where is gets trickey. It works the same way as any other DOF situation with a few snags. I'm not sure how exactly you went about achieving the macro so I'll outline the methoeds I know:
Reverse lens: reverse lense macro with a modern camera leaves your DOF razor thin and there is not much that can be done because to the best of my knowledge the lens can not be set to full manual. Older film camera lenses like the M-42 and the breechlock Canon FD can be set to full manual providing full aperture control and with it greater DOF. If you are using a reverse lens coupler you can use the older lenses provided the filter diameter is the same. For the smaller apertures you definately want a tripod, mirror lock and shutter release delay.
Designated Macro lens: Well that is easy enough, smaller aperture can be used as normal and again, you definately want a tripod, mirror lock and shutter release delay.
Macro filters: DOF is usually thin with those only so much you can widen it with aperture.
I don't know anything about the communications between body and lens with the use of extention tubes so I'll leave that for someone who dose.
You have a sound expariment here, Your subject is a little drab but it was an expariment so I won't count that agenst ya. It is a good first try, I'd like to see more use of it in the future.