Srila Prabhupada answers some questions in a letter to his disciple, Aniruddha prabhu. Aniruddha was a nice devotee who first joined Prabhupada on the West Coast of the US in 1967. I first met him in L.A. in 1972, then 25 years later in Honolulu. Recently Aniruddha passed away in Hawaii. This letter was written by Prabhupada when Aniruddha was still a new devotee. Although email had not been invented and Prabhupada needed to dictate or write and send each letter personally, he never failed to respond to his disciples, and to enlighten them with his pure vision. This is just one symptom of a great devotee.
Regarding your questions: Your first question, "Are great sages put under yogamaya or maya? Also are all the eternally liberated souls under yogamaya?"
Yogamaya means the mercy of the Supreme Lord which connects a devotee in the transcendental loving service of the Lord, and mahamaya means the external potency of the Lord which puts a conditioned soul into illusion that he will be happy by material adjustment. So great sages who are impersonalists are also under the spell of mahamaya, because a conditioned soul in the material world wants to improve his material position as exalted as possible, and the concept of becoming one with the Supreme Lord is the greatest illusion for them. Because it is a fact that nobody can be equal or greater than the Supreme Personality of Godhead, and as such, anyone desiring to become one with the Supreme means that he is still in the trap of maya.
On the other hand, a humble devotee who may not be a great sage, but simply by his implicit acceptance of the Lotus Feet of the Lord as the goal of his life means that he is under the protection of yogamaya. I think this will clear the idea.
Your next question, "Is there a difference between Arjuna's body and his soul, and how does this apply to all Krishna's eternally liberated souls described in the scriptures. Is Arjuna always the same in his appearances with Krishna or is a new soul taking his body each time?"
Yes, there is difference. Therefore he forgets his past activities. Just like we forget ourselves while dreaming because our subtle body acts at that time differently from the gross body. Similarly, by changing this body or transmigrating from one body to another, we forget all the activities of our previous body. The associates of the Lord, even though they have a different body, or even though they forget the activities of their past body, still they are associates of the Lord. These explanations are given in the Bhagavad-gita as it is.
Your next question, "Is a pure devotee eternally liberated and if so is he at any time a conditioned soul? We are eternally conditioned, but as soon as we surrender to Krishna do we then become eternally liberated? When Lord Christ appeared he seemed to be conditioned in his growth. Was he a specific incarnation or a conditioned soul who became liberated?"
You are not eternally conditioned. You are eternally liberated but since we have become conditioned on account of our desire to enjoy materialistic way of life, from time immemorial, therefore it appears that we are eternally conditioned. Because we cannot trace out the history or the date when we became conditioned, therefore it is technically called eternally conditioned. Otherwise the living entity is not actually conditioned.
A living entity is always pure. But he is prone to be attracted by material enjoyment and as soon as he agrees to place himself in material enjoyment, he becomes conditioned, but that is not permanent. Therefore a living entity is called on the marginal state, sometimes this side, sometimes that side.
These are very intelligent questions. And I am very glad that you are putting such intelligent questions and trying to understand it. It is very good. But best thing is that one should know he is in conditioned life and try to cure it. When a man is in diseased condition he should try to get out of diseased condition without harassing his brain when the disease has begun. But it is to be understood that the disease is not our constant companion, it is temporary.
So the best thing is to cure the disease, and not waste our time to find out the date when it began. Forgetfulness of Krishna is the disease, so let us keep ourselves always in Krishna Consciousness, and get out of the disease, that is healthy life. Yes, Lord Jesus was jivatattva. He is not Visnu tattva. When a jiva tattva becomes specifically empowered by the Lord, he is called saktyavesa avatara. Lord Buddha and Lord Jesus Christ were in this group of saktyavesa avatara.. But they were not in conditioned state when they appeared; they came to teach here.