Regarding your several questions: Where are the spirit souls coming from that are taking microbe bodies? It is not a matter of any particular body. These spirit souls and all spirit souls are coming from Vaikuntha, but in these material worlds they are taking various grades of bodies according to their material activities. There is no "new" soul. "New" and "old" are due to this material body, but the soul is never born and never dies, so if there is no birth how there can be new soul?
Your second question: Is there any particular reason why some spirit souls become directed toward Krsna Consciousness in the first place? How does one get on the progressive path of elevation to Krsna Consciousness? The answer is that it is by the mercy of the Lord that one comes in contact with a Spiritual Master Who can revive the dormant Krsna consciousness of the conditioned soul. Krsna is always merciful and He comes Himself, He leaves behind Him instruction like the Bhagavad-gita, etc. and He sends His representative, the Spiritual Master. In this way the merciful propaganda is going on.
Every individual soul has got the discriminating power, so those who are pious they take advantage of this opportunity of the mercy of the Lord. But both pious and impious souls are being convinced by this Krsna consciousness movement. The human being is supposed to be intelligent more than the animals, so the intelligent persons or pious persons are coming in contact with Krsna consciousness.
Regarding your questions with reference to B.G. III,5, and the Vedic hymn quoted in the purport to B.g. 14.15 and the statement ". . . when the living entity is bewildered in his desires, the Lord allows him to fulfill those desires . . ." You have quoted, "The Lord engages the living entity in pious activities so he may be elevated. The Lord engages him in impious activities so he may go to hell . . ." So that is also originally the individual soul's desire and as Supersoul the Lord is giving everyone the opportunity to go to heaven or to hell or to Vaikuntha if he so desires. For those who are hankering after material opportunities the Lord as Supersoul is giving them the opportunities to enjoy the material nature and the facility is being supplied by the material nature.
Similarly, a living entity who is desiring for spiritual upliftment, the Lord is giving him the opportunity of the Vedic literatures and the Spiritual Master. But His advice to all living entities is to give up all nonsense and everything else and surrender unto Him. The living entity by accepting one kind of opportunity is going to hell and by accepting the other kinds of opportunities he is going back to home, back to Godhead. So both opportunities are offered by the Lord. Therefore indirectly you can say that one is being sent to hell and one is being sent to the spiritual world by the Lord—but He is simply supplying the opportunities to everyone as he desires. The intelligent person therefore does not desire anything—he simply surrenders unto the Lord or he desires to serve the Lord and that is his greatest opportunity.
"Man proposes and God disposes." That is the sum and substance. But as a pure devotee of the Lord you should not propose—simply accept His proposal and surrender unto Him. So far the conditioned soul is concerned the same opportunities are there, but if he does not take advantage of the opportunity to elevate himself to Krsna Consciousness and chooses to misuse his independence for taking the opportunity to enjoy some material happiness, then he will remain conditioned as the Lord will allow him to fulfill those desires. The opportunity is always there, just as we are offering so many ways to become Krsna Conscious, but if you don't take the opportunity what can I do. That is purposeful negligence of duty. The example may be given of a man who is sleeping. If he is actually sleeping, he may be wakened by various means, but there is no doubt that he must wake up. However, if a man is pretending to be asleep there is no way at all to rouse him up.