Hi Dave,
Thanks. Your procedure for using the meter sounds great to me, though you don't have to worry about drying the distilled water from the probe before using it for the test. I know some of these probes are much more robust than the ones I was used to using, but the less physical activity they have to endure the better they like it. Kind of like me in that respect I guess.
The problem with the proteins, in particular, and the lipids (fats) is that they aren't very soluble in water, they like to stick together and they like to stick to membranes. Since it's generally not recommended, at least that I have seen, to use soaps or detergents on pH probes and you shouldn't spit polish the membranes either, you have to come up with something that does the job in a gentle and neutral sort of way. Urea molecules (found in urine, hence the name) are neutral, but they are sort of funny little creatures. They like to play ring around the rosy with proteins and fence them into a little container they build called a clathrate. You can look it up if you are bored beyond tears. This solubilizes the proteins and allows them to drift away into the water solution and thus clean the membrane. The NaOH solution (sodium hydroxide, Drano) turns the lipids into free fatty acids which are soluble in water as well. Actually it turns them into soap, but the quantities are small. Those are the two main problems I would foresee with whey. This was not a trivial problem with the research grade probes I was using. I had to redo whole experiments where the pH of the buffers I made was off by a point or more, ie. 6 instead of 7, because a previous user had spent an hour or two testing cell cultures or cell culture media and had not cleaned the probe with urea or labeled the meter as contaminated and not to be used without cleaning.
Urea is readily available online or maybe even at a camera shop where they sell developing supplies. If they still do that. I don't think you need the highest grade or even food grade as you will rinse it and any soluble contaminants away from the probe when you rinse it in distilled water after cleaning. And it is pretty much not hazardous. I guess you could water your houseplants with the leftovers if they are looking a little pale.
Hope this helped,
Michael