My suggestion would be to start by focusing on hypotheses that your illness has a single cause that is short-term, like a matter of minutes, hours, or at most a day. And also that it’s reliable—do X and Y happens, almost every time. These assumptions are easiest to rule out and do not require elaborate tracking. You may also want to focus on expanding your hypothesis space if you haven’t already—food, exercise, sleep, air quality, pets, genetic and hormonal issues, and chronic infections, are all worth looking at.
As you noticed, testing more complex hypotheses over long time scales makes the process of gathering evidence more costly and slow, and the results become less reliable due to the risks of confounding and the number of post-hoc tests you will be running.
My suggestion would be to start by focusing on hypotheses that your illness has a single cause that is short-term, like a matter of minutes, hours, or at most a day. And also that it’s reliable—do X and Y happens, almost every time. These assumptions are easiest to rule out and do not require elaborate tracking. You may also want to focus on expanding your hypothesis space if you haven’t already—food, exercise, sleep, air quality, pets, genetic and hormonal issues, and chronic infections, are all worth looking at.
As you noticed, testing more complex hypotheses over long time scales makes the process of gathering evidence more costly and slow, and the results become less reliable due to the risks of confounding and the number of post-hoc tests you will be running.