I used to have(and I think still have) a scientific mind too.I am a master student of physiology.and lots of similiar expriences to yours made me realize that my models were just made up and non existent.the brain is creating my expriences?brain is just made up of matter.even signals in the brain are being created by movement of Ions(matter).these are what science says.but then,what is matter?! nowadays its so obvious to me that all of this is just a model.feeling,seeing,hearing... these are not movement of ions!
The questions that you ask are very good questions and deserve time for contemplation.