We have covered the topic of waswasah and doubts in tahara a few times, and you are able to search in the Q&A on the topic of waswasah and taharah.
The simple rule of thumb is because you are doubting, you consider it all to be tahir. Nothing more.
Please watch this clip, which is a part of a lesson I gave on taharah and najasah. Hope it will be of benefit.