Focus stacking - selecting focus areas

I am trying to learn focus stacking. Here is a trial I did on a couple of pomegranate fruits. Although this did yield a picture better than what I had hoped for, I realized that my planning for the session was not good. I ended up taking too many shots and then had to forage for sharper areas within the frames one by one. Also some areas remained blurry. I realized that I could have done a bit of planning to pre-determine areas of the object to be focussed on manually and then execute that plan. For example - put a 3x3 grid on a sample frame to start with and mark the areas within the nine blocks which should be focussed on. Not a perfect process, but might yield a better and fewer selection of pictures to stack. The challenge also seemed to be to estimate the depth of field across the object and make appropriate focal distances adjustments.

Question - Are there any guidelines/processes/practices for systematically improving the coverage of such objects for focus stacking?

(I am using RT 5.8/Gimp 2.10.19 on Ubuntu 18.04. Focus mask of RT was a great help, and so was the batch/queue processing.)

You should check out https://github.com/PetteriAimonen/focus-stack

@andabata says it fails on hundreds of images, but we should work to improve it, since the core is there and seems good.

Manually brushing in that many layers for a focus stack seems like a lot of work.

Thank you. Will check this out.