One feeding trough has a width of 36". another feeding trough has a width of 96". what is the percentage difference between the widths of the two troughs?

Percentage difference is always relative to one of the items.
I.e. the factors are either 36/96 or 96/36.
If the reference is the 96" width, then difference is 96-36=60, and the percentage difference is 60/96=5/8=0.625 or 62.5%
If the reference is 36" (yes, usually the first mentioned item), the difference is still 60, but the percentage difference is 60/36=5/3=166.7%