The central question you say is "where is the soul and where does it come from?" That is not difficult to understand. We've already discussed how the soul is residing in the heart of the living entity and that it takes shelter after death in another body. Originally the soul comes from God. Just like a spark comes from fire, and when the spark falls down it appears to be extinguished. The spark soul originally comes from the spiritual world to the material world. In the material world he falls down into three different conditions which are called the modes of nature. Just like the spark of fire when it falls on dry grass and the fire quality continues. When the spark falls on the ground it cannot display its fiery manifestation unless the ground is favorably situated. Similarly when the spark falls on water it becomes extinguished. As such we find three kinds of living conditions. One is completely forgetful of his spiritual nature. One is almost forgetful but still there is an instinct of spiritual nature, and one is completely in search of spiritual perfection. There is a bona fide method for the achieving spiritual perfection by the spiritual spark soul and if he is properly guided then he is very easily sent back to home, back to Godhead where from originally he fell down.
It will be a great contribution to human society if this authorized information from the Vedic literature is presented to the modern world on the basis of modern scientific understanding. The fact is already there. It simply has to be presented for modern understanding. If you desire, I shall give you more information in this connection and you can present it in scientific words. If you so desire, you can publish this letter in the paper also.