This may seem so obvious, but it was a revelation to me (and I thought of it myself): As I strip the bike of tanks, plastic, fairings, etc, I will keep the fasteners in the appropriately labeled bins of a fishing tackle box.
Also, my new AGM battery is shorter than the non-AGM battery it replaced. It sits snugly in a hole and is almost impossible to grip in order to pull it back out. Solution: strap a large zip-tie around it. Doesn't take up any space in the cavity and is just enough "handle" to lift out.