Nikonian 72: I thought I had your hand held technique figured out until you said 'why I shoot A-F". I thought you set focus to manual , turned your lens to 1:1, then moved in on subject til in focus. Do you look at distance scale after each shot to verify that you were at 1:1?
This thread is an exercise for OP, who has NO A-F with her Nikon D3000 and a manual Vivitar 100-mm macro lens.
I still own my Nikkor 55-mm macro lens, purchased in 1972. Strictly manual. I now use it for tabletop macro work.
I purchased a Nikkor 105D to use manually with my Nikon D5000. I was not happy with my inability to capture consistent focus. I upgraded to a Nikkor 105G (built-in motor & VR2). I also added a D90. Very happy now.