Normally the number of shots can be calculated by dıvıdıng object sıze by DOF ın mm and multıplyıng by factor of 1.3 to allow for overlapping. For example, flower 100 mm / DOF 5 mm * 1.3 = 26 shots. This is rough estimation, the final decision should be made by looking at the resulting image - there should be no out of focus strips between well focused areas. I think your troubles are cased by parallax and other factors, not by small DOF.
My cognisys extended macro rail seems to be moving less than i expected. when i set 10 steps of 50 mm I get an actual movements of the camera of 50 mm rather than 500 mm. Some of my issues are starting to go away.
Please see what size of the step is set for StackShot in Helicon Remote preferences. It might be 0.1 mm by default.