Soul is a conglomerate and not a unit as thought by many. It has four parts namely Buddhi, Ahankar, Manas and Chit. They need to be purified thoroughly so that link with the Divine is established. God has willed that all should be happy and contented, it is only we with our attachments created problems for ourselves.

Ecstasy of Soul
1. Regarding the nature of the Soul:
I am sure you have read Rev. Babuji's clarifications on the Identity. There are three concepts 1. Soul 2. Identity and 3 Individuality. My experience is that the individuality is a composite of Ego, Manas and Buddhi with all their hues (Sattvic, Rajasic and Tamasic). You will note that all our relationships, the concepts of runa(debts) are included in this. And that is what is reborn based on the choice of this faculty to undergo certain portion of the karma's during the immediate next life and this is what transmigrates but as only part of the Karma's are sought to be cleared in a particular life, the result of quite a lot of karma remains to be undergone normally during later lives. Due to sadhana, first we stop forming further samskaras by total dependency on the Master, and the Karma that we have opted to undergo during this life is gone through as also the balance of Karma that we have proposed to undergo later in the next lives also are undergone either during meditations or during dreams. However it is necessary that the bhog of all previous Karma's should be gone through before we come up to the stage of mere identity from the level of individuality. You are aware that unless the help of the Master is there through Pranahuti and we attend to the cleaning methods and meditation on points A and B as given by the Great Master regularly the bhog cannot be completely gone through and the consciousness becomes Nistrigunya. The identity as different from individuality has only consciousness as its body, while the individuality is invariably a conglomerate of sense organs, motor organs, Manas and ahankar. However my experience is that while simple and silent identity is felt it is also accompanied by the feeling of devotion to Master, Perhaps that is the nature of the Soul or identity, namely to be devoted to Master with total simplicity. No emotional overtones are there. No ecstasy is there. No prayers are there. It is just an awareness of being. Master perhaps refers to this when he says neither the beggar, nor beggars bowl is there but only begging. I do not know how to express it better. The Soul or identity is mere consciousness of nothingness. Neither the idea of vacuum nor the idea of space is there. There are no thoughts but simple awareness of nothingness. It is neither a bubble nor water but the memory of having been a bubble. I do not know whether what I have written makes the matter any clearer but that is what I know. While the devotedness and dependency are felt during the meditations, in actual day to day life this consciousness can take only the form of service to Master (kainkarya) and any other form of expression of this is only a residual effect of the individuality, These states are the agony and ecstasy of the Soul.

God
As for God, I never sought nor am I interested. Except the Kaushitiki Upanishad no one has described God and His land, all others talked of Brahman. Our Master leads us to Nothingness through Brahmagati and nothing more. If we cling to our pet notions of God and His manifestations however great they may be I am of the opinion they are sufficiently heavy and the heart feels loaded with some stone.

1. I am always told (and convinced) that God is the first priority, Divine work including sadhana must always override all other things. I am trying to give sadhana high importance, I know I am not successful all times.
I do not want to dwell about God as a goal of life as no one for sure can explain anything about it to others. I think you need to read the book Ten Commandments of Sri Ramchandra.

2. Another shortcoming on my part is that I am still not able to accept the Master in toto. I still see difference between God and Master
Neither you know the Master nor the God then why do you bother about their difference

Atman and Brahman
Atman and Brahman first of all are not entities but only conglomerates. Atman consists of Buddhi, Manas, Chit and Ahankar. So long as these faculties function moving in a limited sphere it is called Atman. When the same conglomerate grows by its functions (obviously thought) it gets called by the name Brahman. Atman from its initial state of thinking and moving in its sphere grows first into the stages of Rishi, Rajarshi and Brahmarshi. Paramatman is the word that has been usually used in Religion to note the first and foremost expression of the Divine and is not a stage of the Atman. I do not know whether you are clear about these concepts.

Ego
The Ego is not something that goes before getting into the higher realms. But that is what we were asked to learn. That Ego is different from the development of Ego through the rings of Egoism that Master talks about.
I am not able to understand the demand to know everything. Certain things are better not known: that is the system of Rev. Babuji. He in His wisdom has saved us from knowing everything, lest it develops EGO. Still you want to know because it is said so in tradition or in scriptures. If He spoke with authority He has the authority. Is it not enough that we are humble servants of the Master? Is it too small? Don't you think your craving in this regard is a product of ego? Please do not misunderstand. I am only trying to tell you our limitations and the limitations imposed by the Master on our work. What is the value of knowledge if it is not for action. When He says He uses us for His work without our conscious knowledge and will do you still feel that you are to get that awareness? Don't you think that the so called dissatisfaction arising out of this is only a fiction of the Ego? Having reached high states of consciousness and spiritual development it is only service to the Master that counts.

1. Trying to feel lowliness and develop humility under all circumstances, but sometimes ego springs up and doesn't allow it. Praying to the Master for nullifying the ego.
What you mean by ego is not clear. Ego has three types of expression- that it is the doer, it is the enjoyer and it is the knower. If all these three are converted to mean Masters' ego gets molded. And at the perfect state it becomes identity. Never is it annihilated. Annihilation of ego is the talk of vedantins and pseudo yogis. Please find time to learn the system well.

2. Feelings of Doership
Our ego has basically three components: 1. I am what I do 2. I am what I achieve 3. I am what is my reputation. One has to come out of these and that takes some time; assiduous practice and dependency on Master are the means.