You are right, those roots look healthy. And the soil looks wet. When you repot, don't water for a week or more to allow damaged roots to heal.
Watering to soil saturation is good, soaking for 1.5 hours is bad. When you simply add water, does the soil get completely wet? You can figure that out with your stick by looking for wet and dry patches on it.
Look at the growth of your cactus. The new growth should be as wide or wider than the old growth. If there are narrow spots, those will be weak spots and the cactus will bend or break from the weight of the new growth above it. It could be the wilted wrinkly top just isn't getting enough moisture from the roots because of the narrow little connector piece.
