***Is there a one to one correspondence between someone's thoughts and the physical state of their brain, such as the positions of cells and the electrical states of neurons?***
I'm not sure, but it seems there are some unsolvable problems. For example, what is the cause of a mental action? If that cause is some physical state, then what about cases where we do something because of some particular reason (e.g., tie our shoe because our shoe has become untied). If 'we' decide to tie our shoe, then the cause is mentally causation and not physical causation. However, this somewhat contradicts the premise that a one for one correspondence between physical states and mental states. That is, the mental determines the physical (our action to tie the shoe). Some philosophers, such as Donald Davidson, have rejected this strict reductionist usage of psychophysical laws (called bridge laws) and have opted for a term called supervenience (i.e., there is a relationship between physical to mental, but it cannot be classified as a set of bridge laws that determine that relationship).
***If so, would it be theoretically possible to "program" someone to think a certain thought by manipulating their physical components?***
Yes, that would be one of the implications. However, if the mental state can program the physical state (e.g., by learning to be positive, etc), then couldn't the mental state re-program themselves to reject the embedded thought?
***Could there be a "collective consciousness" to the universe that none of us are aware of?***
Yes, there could be.
***If not, does the thought really exist in the physical world? I'm curious to see what opinions people have.***
Thought looks likely to exist as a physical result of something happening in the brain. Otherwise, what use does the brain provide?
Warm regards, Harv