Difference between seed, nut, kernel, pit, grain

Not sure this is a good question but basically they all refer to part or whole of a particular seed. Apples have pips. Bean can be the shelled or unshelled product or the whole plant. Kernel can also mean just the inner soft part of a seed where there is a hard shell. There's also "stone" and others. Grain can refer to the seed or the whole grain food group. All seeds can be further classified and disected to reveal more part names. I really don't understand where your question is going. The terms you mention have related but also specific meanings within biology and otherwise.