And there's also that tiny problem left over from quantum mechanics about whether or not perception changes the workings and outcome of an experiment.

So at this point assuming that thinking is physical is a supposition that can't be proved or disproved.

In metaprogramming terms you're chunking information more or less in behavioural terms, and - as long as you don't get impatient - that's all you need to do. There is no complete functional disassembly of minds, souls, thoughts or even brains to refer to, so it's impossible to state categorically that X, Y or Z are the cause of any inner experience. You can't even do this with drugs. Just because the effects of LSD or ayahuasca are fairly reliable, doesn't mean anyone really knows what they change, or how.  

All you can do is give the black box a prod every now and then, try to learn from what it does, and look at other people's incomplete ideas about how to make changes, and the kinds of changes that can be made.