Once the problem became recognized, the company would have provided the information somehow, and the "somehow" varied from RR to RR. Beyond a rule in the Book of Rules about needing to know about restricted cars in a train, it would be the last place CI wheels or car numbers would be listed because this information changes so rapidly. SIs, ETTs, etc. are frequently updated, the Book of Rules is not.

The problem didn't become recognized and accepted until well after WWII, and once the RRs figured it out, they arranged for the AAR to ban CI wheels (in 1958). Last time I checked the calendar, the 1940s predated the 1950s, let alone 1958, which means your 1940s era stuff is dated, and undoubtedly doesn't contain the strictures against CI wheels. You just don't get it do you?

And no, CI wheels weren't stamped, the letter and numbers were in the molds used to cast the wheels, usually appearing just inside the rim on the front or rear side of the plate (and not all types of CI wheels had the ribs on the back). Until well into the mid 1970s, the car departments went over each train before they left yards, and it's they who looked for this sort of thing. By the 1970s, CI wheels had pretty much disappeared, and they forgot how to recognize them, which is why in the late 1980s a friend and I were able to move a boxcar which had three axles of them over a Class I carrier.

I recall those yellow and white dots you mentioned. They indicated whether the car department had found 3-riser wheels on a car. This had to do with increased internal stresses leading to wheel failures and were a result of an inadequate system of risers used in the casting process.