There is one thing I think that was missed... I didn't read ALL the comments but I didn't notice anyone advising you to put a turbulence shield around the probe. Typically it is a piece of PVC pipe about 30 cm long assuming a 6 Cm probe. Your issue (and one of mine when I was working on a similar project was simply that any salt (of any kind) concentration in water will never be completely homogeneous), there will always be 'strata' of slightly different ionic concentrations of the solute and solution. The variances are statistical noise in that they will average out when the solute is used for it's intended purpose... even though a PH measurement is Logarithmic in nature and specification the average PH will be equal to the undisturbed sample... I think that you noticed in your measurements that the ""Sample" from the tank was usually the same number or very close to it while the tank measurement differed. PH measurements depend on the scope of the measurement and the measuring conditions, Your measurements will average out... make them at the same conditions every time to get the true value and eliminate conditions that could cause variances in the measured media... Thus a piece of PVC pipe and some more math to as I remember calculate the Mean Value of several measurements based on the use of the media being measured better to take a set of measurements, calculate the mean value and then repeat the measurement as outside conditions dictate probably when any changes have had time to reach equilibrium ... Chemical processes and use are typical variables as is temperature and flow about the probe. I think you have everything done except modifying the 'flow' about the probe and the measurement statistics. Your process seems to be well in hand however and I (for one) Applaud your hard work... IMO...
Doc