From time to time, there has been talk, about what the proprietary PDAF functioning actually does. Does it hammer home to "close" and then perform a corrective fine adjustment? I don't know, but if so could AF-S lenses have an ability for the corrective cycle that screwdriver do not? Anyhow, I'm not asking for a serious answer, just thinking out loud about changing one variable (screwdriver for AF-S) to see if a difference could be measured in your unit.
Another stupid question on my part but what if you try AF-C - does it make any difference? I am biased enough that I do all my photography with AF-C not AF-single (but that is not a majority view as I believe all advice is tune while using AF-single).
Regardless your sad saga here may be approaching the "argue with them to get a replacement" stage as you've been through enough perhaps.