I don't know why you are fiddling with cleat fore-aft adjustment. Stack height differences in the shoe sole translate into moving the seat up or down. It's as though you are increasing or decreasing the length of your crank.

If the stack height is the same on both pairs of shoes you use, then you do need to measure the distance of the slots or holes from the effective heel of your shoe to determine whether they are in fact in the same position on both pairs. Then you can decide the position of your cleats. The "effective heel" is where the back of your heel rests against the inside of the shoes -- measuring from the back of the heel on the sole is pointless, as is measuring from the toe back to the slots. Like measuring stack height, it is not an easy thing to do.

I have a similar stack height issue with a pair of Shimano sandals compared with my other shoes, but I don't bother making any adjustments -- I don't ride with the sandals for long enough distances to make the difference an issue.

From the symptom you discuss in the opening post, you may have length length discrepancies with your right leg shorter than the left. You should get this checked by a physiotherapist or if need be, through Xray. The physio check is pretty simple. The solution is a little less simple, but may involve cleat shims, orthotics or in an extreme case, using cranks of different lengths to compensate.

Do you have lower back pain in everyday life?