In answer to your several questions, first; what is meant by conditioned sould? Conditioned soul means one who has accepted something illusion as reality. Conditioned means that due to imperfect desires the spirit soul becomes dependent on material conditions for his satisfaction.
Your second question; how does he become conditioned when the jivatma is eternal full of bliss and knowledge? The answer is that it is not the soul itself that becomes mixed with matter but it is his consciousness that becomes absorbed in trying to enjoy the matter. Out of desire to lord it over, the jiva soul forgets that he is eternal, full of knowledge and full of bliss and identifies with the material energy. So it is the consciousness of the conditioned soul that is affected.
Your third question is: does the soul ever become weak or strong on account of its association and contact with material nature? It is not the spirit soul that becomes weak or strong but it is his determination to become Krsna Conscious that me become weak or strong. By the influence of the modes of passion and ignorance he becomes weak and by the influence of the mode of goodness he becomes strong. But by the association with the pure devotee he becomes strongest.
Your fourth question: "Whether or not it is possible for the soul to exist without having this external gross and subtle body covering it? So if the bird is existing within the cage and someone takes away the cage does that mean that the bird can no longer exist? No. This body is illusion. It is only because of out attachment for this body that we have to remain within it. But as soon as one transfers his attachment to Krsna then no more is there any need for this body.
Your fifth question is, "Bhagavad-gita says that the conditioned soul is subjected to four defects. Does that refer to the body or the soul?" The defects are there in the living being when he is acting on the material platform.