Thank you for your question. Shirk is to limit Allah in any way such that even the conception of another god would be possible. Even to say He is a god is not satisfactory as that would entail a genus of gods under which God would be a species with only one referent. Numerical oneness is limited, as in numbering God as one a person gives the possibility of two gods. Numbers themselves are a factor of the material world. Rather, Allah is above being numbered as a number entails a limit and He is above all limitations.
As for prostration, it is clear that if a person prostrates to a being in worship then that is completely forbidden in Islam and Shiism as a sect within Islam. However, prostration does not only entail this meaning and is also a symbol of humbleness. For this reason God commanded the angels to prostrate to Adam (as), not in worship or out of polytheistic intent. So too Prophet Ya'qub (as) prostrated in front of Prophet Yusuf (as).
May you always be successful