The previous post from this work will be found here.
Then said Mary to the Angel, How shall this be, seeing I know not a Man? Whereunto the Angel answered, The Holy Ghost shall com upon thee, and the Power of the Highest shall overshadow thee, therfore also that Holy Thing which shall be born of thee shall be called The Son of GOD.
I praise and magnify the Name,
O thou Son of God,
for thine infinite condescension to become the Son of Man.
It is not less Blessed and Mysterious to conceive Thee in the Heart by Faith,
than to carry Thee in the Womb of Flesh:
Send therefore, I beseech thee,
the same Spirit and Power to rest upon mine Affections,
till Christ be formed in me,
that thy Humility and Holiness,
thy Life and Love,
may be brought forth in my conversation,
and so adapt me to be called the Son of God.
 While my search is limited, the earliest I could find this exact phrase was in John Owen, for whom it was a favorite. For example:
We may behold this glory in his infinite condescension to take this office on him, and our nature to be his own unto that end. It did not befall him by lot or chance;—it was not imposed on him against his will;—it belonged not unto him by any necessity of nature or condition, he stood not in need of it;—it was no addition unto him; but of his own mind and accord he graciously condescended unto the susception and discharge of it.
Owen, John. The Works of John Owen. Edited by William H. Goold, vol. 1, T&T Clark, p. 323.
The phrase was picked up Jonathan Edwards, who also used it frequently. It would seem then, as a tentative possibility, that Traherne and Edwards got the phrase from Owen.
 Traherne is here playing on a pun on the word “conceive”. It can mean the physical conception within a mother. It can also mean an intellectual apprehension of a thought. The idea here is as follows: The miracle of Jesus’ birth from Mary was a miracle beyond belief. And that Christ should be made in us, that we would partake of his life is equally blessed and inconceivable. This will be a theme worked out in the prayer.
As for the pun, Shakespeare had used the pun in the opening scene of King Lear.
Act I, Scence 1, King Lear. Glouchester has just introduced his bastard son to Kent.
Is not this your son, my lord?
His breeding, sir, hath been at my charge: I have
so often blushed to acknowledge him, that now I am
brazed to it.
I cannot conceive you.
Sir, this young fellow’s mother could: whereupon
she grew round-wombed, and had, indeed, sir, a son
for her cradle ere she had a husband for her bed.
Do you smell a fault?
 The prayer here may be understood by a reference to the slightly earlier work of John Owen:
First, The pattern which we ought continually to bear in our eyes, whereunto our affections ought to be conformed, is Jesus Christ and the affections of his holy soul. The mind is the seat of all our affections; and this is that we ought continually to design and endeavour, namely, that the “same mind be in us that was in Christ Jesus,” Phil. 2:5. To have our minds so affected with spiritual things as was the mind of Christ is the principal part of our duty and grace; nor do I think that any man can attain any con siderable degree in spiritual mindedness who is not much in the contemplation of the same mind in Christ, 2 Cor. 3:18. To this purpose ought we to furnish our minds with instances of the holy affections that were in Christ, and their blessed exercise on all occa sions. The Scripture makes a full representation of them unto us, and we ought to be conversant in our meditations on them. What glorious things are spoken of his love to God and his delight in him, whence also he “delighted to do his will, and his law was in the midst of his bowels,” Ps. 60:8,—seated in the throne of his affections! What pity and compassion had he for the souls of men, yea, for the whole human kind, in all their sufferings, pains, and distresses! How were all his affections always in perfection of order, under the conduct of the spirit of his mind! Hence was his self-denial, his contempt of the world, his readiness for the cross, to do or suffer according to the will of God. If this pattern be continually before us, it will put forth a transforming efficacy to change us into the same image
Owen, John. The Works of John Owen. The Grace and Duty of Being Spiritually Minded. Edited by William H. Goold, vol. 7, T&T Clark, pp. 467–68.
 Paul writing to the Galatians, “my little children, for whom I am again in the anguish of childbirth until Christ is formed in you!” Gal. 4:19.
 All conduct, not merely speech.
 “28 And we know that for those who love God all things work together for good, for those who are called according to his purpose. 29 For those whom he foreknew he also predestined to be conformed to the image of his Son, in order that he might be the firstborn among many brothers.” Romans 8:28–29 (ESV)