He was not in prison, but his exile felt like a prison.

We do not know exactly what his "extremities" were, but they included his loneliness, separation from his congregation, and his being forbidden from preaching.

He was exiled because he opposed the changes forced upon the Church of Scotland by the English. A modern person might think that Rutherford was making too much of what the English wanted. However, Rutherford felt that the Bible was the only rule of worship. He was willing to suffer and die for Scripture.

That is, elders in the Church of Scotland who caved in under the English pressure.

"You have made my days a mere handbreadth; the span of my years is as nothing before you. Each man's life is but a breath." Psalm 39:5 (NIV)

He is probably referring to himself as a prisoner, as well as all of us a "prisoners" in the flesh. In heaven we will be completely free.

Death is often referred to as a river. Heaven is the "other shore."

"So you are no longer a slave, but a son; and since you are a son, God has made you also an heir." Gal 4:7 (NIV)

"In my Father's house are many rooms; if it were not so, I would have told you. I am going there to prepare a place for you." John 14:2 (NIV)

That is, in his separation from them.

"No man shall ever behold the glory of Christ by sight hereafter, who does not in some measure behold it by faith here in this world." John Owen

Rutherford may be referring to two things. First, he was the pastor settled by the Presbytery and the consent of the congregation, not the man there now. Second, he believes that it is the function of the magistrate to uphold and support the Kirk and Presbytery, not to impose arbirary measures upon them. Note how this is different from the modern view.