Certainty and Skeptical Investigation I know Buddhism promotes skeptical investigation, and finding things out with a personal conviction about them, i.e. not believing the Buddha on hearsay but rigorous examination. 

I wonder: how is such a certainty achieved? I would think the combination of shamatha and vipassana is the answer, but I wonder what EXACTLY is the closest determinant of a feeling of certainty, whether sensory (seeing something and feeling quite certain of the perception) or cognitive (feeling certain of some analytical reasoning). 

Personally, I feel like I often achieve a feeling of certainty, but it usually fades into doubts and alternate hypothesis. I can't seem to generate a sturdy sense of truth. 

I appreciate any answer to this question.
Thank you.
Thanissaro Bhikkhu explained this very well in one of his works, can't find the link at the moment. He said, Liberation is more like a hands-on skill than a pure sterile insight. As with any skill, the understanding and the dexterity grow in lock-step supporting each other. You learn through trial and error, and as you watch the results of your attempts, you infer the mechanisms at play. At the same time, you study theory - explaining the mechanisms - which sheds light on your practice. 

Certainty comes as a result of having acquired the skill. This may or may not come from theory, and may or may not be something you can explain in words. Conceptual model is the optional part that aids one's practice and helps transmit the teaching forward, but cannot give the sense of certainty by itself.

In Vajrayana schools, certainty also comes from the lineage blessings through a ritual known as empowerment (abhisheka).