You have an interesting project there.
Besides researching the various patents developed for stock cars, you may also need to check on the related aspects of how cattle, hogs, etc. were handled while on their way to packing houses.
One of he first issues I think concerned animal safety while being transported: how many to a car, how much room they had within to reduce the prospects of injuries and death.
Another was adequate rest, especially for long distance transport. As things developed, beef cattle had to be given rest stops along the way, where they were unloaded from the cars and put into feed lots for a specific period of time. This rest, with available feed and water reduced the stress of travel, which led to weight loss. It also provided an opportunity cull out animals showing signs of disease or illness.
One transporting hogs by rail, they too required rest periods as well as being hosed-down, especially in hot weather to keep them cooled. There were hosing stations, where water hoses (as large as like fire truck hoses) sprayed water into the hog cars as they slowly rolled by.
While some patents on the surface may have seemed like a good idea, it would well be that in practice they did not work out all that well. Water troughs might be one of them, in that water would be consumed and also sloshed out in transit from the way the cars rode or the train they were in was being handled. Also, animals confined in the could possibly soil the water troughs with their solid and liquid wastes. Water troughs would therefore need frequent checking, cleaning and refilling along the way. And sadly, even back then, employees did not always follow through on details if weather was bad, the train running late, or other matters taking a priority. It may well be that rest stops followed after on board water troughs were not successful.
Better treatment for animals in transit was a gradual development, coming about at first because of losses from injuries, disease and sometimes death. Then too, the issue of weight loss between loading and arrival at packing plants. In those case the bottom line dictated better treatment was needed. Then, there was the development of humane societies dedicated to animal safety and health.
An interesting field of transportation research!