What is the ruling on doubting the ritual impurity (najāsa) of something, then later becoming certain of it, and is it obligatory to purify everything that it touched while there was initial uncertainty about its impurity, and is everything thereby considered pure or not?

The basic principle regarding things is purity. So, if you doubt the impurity of something, its original state is purity. If you are afflicted with obsessive doubts (waswasah), you must strive against them and disregard them. If you touch something you believe to be pure, and then become certain of its impurity, you must purify whatever became contaminated by contact with it, provided that one of the two contacting surfaces was wet or moist. However, if both were dry, impurity does not transfer. You are not required to purify something about which you doubt the transfer of impurity; rather, you are only required to purify what you are certain has become impure.