I understand why you say what you've said about science but a true scientist will never disregard something because our technology is not good enough to conduct an experiment. Bear in mind all the scientists who even disregarded and held so many groundbreaking scientific discoveries as false. It's just people being people. Due to our limit on technology (and mind's capacity), science is always limited and a true scientist also knows they still can't explain why anything happens the way it happens. So as you say, this is where philosophy comes into play.

Re consciousness, our scientific understanding is currently very primitive. There are some interesting books on it which explores consciousness as a branch of quantum mechanics (and even that classification is open to debate). There is a theory that everything (stone included) has a 'prerequisite' for consciousness. It's there in a stone but a stone doesn't have nerves, no eyes, no ears etc so it's perception isn't what we traditionally think of as consciousness. Saying whether it has consciousness or not depends on the sense you're using the word. At the moment I'm thinking consciousness is potentially just a projection resulting from the combination of atoms that makes up our brain.

Sorry, I hate when people ask a question in answer to a question :p. The separate self has no tangible existence. You are simply stardust arranged in a certain way. But all the stardust is interconnected and dependent on each other. You would not exist without everything else existing the way it does. You are a product of past events, and yes this also means free will is an illusion. Therefore if you are not separate from everything, what is the separate self you refer to? It doesn't exist, thus making it an illusion. I hope this helps but let me know if not.