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It's not bad, but just a few points in an attempt to help out:
'Thinking' implies a conscious function which would therefore not be considered a 'sub' conscious level.
When discussing perception from a bio/physiological perspective, perhaps it's best to bring it down to the micro-level of quantum mechanics and discuss the role of the observer in the wave/particle debate whereby subatomic particles witnessed under the intensity of our highest powered microscopes seem to change shape depending on the thoughts of the observer so that the very parts (subatomic particles, or quanta) which form our reality itself are limited by modes of perception or observation.
From a psychological standpoint, we cannot be separate from our 'mind', and there are studies which have proven that the mind itself is not the restricted function of specific chemicals and organs interacting within the human body (i.e. the brain) but rather presuppose an existence of some form of matrix. People with significant brain damage or loss have been noted as still having the capacity for thought and conscious functioning.
Because all of our visible and physical stimuli are the responses of our perceptive feedback mechanisms, both within the mind and body, and yet only capture a fraction of the spectrum of what exists 'out there', surely and truly what we see and witness can only be an extension of not only the perceptive framework of our biological and physiological functions (i.e. our 'ability' to perceive), but are also deeply impacted by our psychological state of mind and how our thoughts, beliefs and emotions color an event.
You have good examples, and just as the very premise of your paper asks, the answers you receive will certainly reflect the personal bias of each person rather than a definitive philosophical 'truth'. Good luck
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