How does The Shepherd and the Sheep illustrate Yeshua the Messiah and Universal Church?

The major passage for the first illustration is John 10:1-39, which contains the discourse on the Good Shepherd.

1. Ten Specific Points
All together this passage makes ten specific points.

First, John emphasized that it is the Messiah who came in by the door in verses 1-2: Verily, verily, I say unto you, He that enters not by the door into the fold of the sheep, but climbs up some other way, the same is a thief and a robber. But he that enters in by the door is the shepherd of the sheep.
The point of these verses is that Yeshua came in by the true door. Anyone else who came in by some other way showed that he was not a shepherd, but a robber.

The second point is that the true shepherd will always be followed by those who are truly the sheep according to verses 3-5: To him the porter opens; and the sheep hear his voice: and he calls his own sheep by name, and leads them out. When he has put forth all his own, he goes before them, and the sheep follow him: for they know his voice. And a stranger will they not follow, but will flee from him: for they know not the voice of strangers.
Later in verse 14, He stated: I am the good shepherd; and I know mine own, and mine own know me.
The true shepherd will be followed by those who are truly his sheep; they will not listen to the voice of a stranger.

The third point is made in verse 7: Jesus therefore said unto them again, Verily, verily, I say unto you, I am the door of the sheep. Not only did He come in through the door, but He is also the door of the sheep.

The fourth point is that He loves the sheep.

And the fifth point is that He provides for the sheep. That is all part of the Good Shepherd motif of verse 14. In His role as the Good Shepherd, He loves the sheep, and this love is expressed by making provision for the sheep.

The sixth point is in verse 8: All that came before me are thieves and robbers: but the sheep did not hear them.
Again, other shepherds are naturally false, and the true sheep, which is the true Church, will not follow a false shepherd.

The seventh point is in verses 9-10: I am the door; by me if any man enter in, he shall be saved, and shall go in and go out, and shall find pasture. The thief comes not, but that he may steal, and kill, and destroy: I came that they may have life, and may have it abundantly.
There is fellowship between the shepherd and the sheep; they have a relationship with each other. Because of this fellowship, they will not be fooled by those who are impostors.

The eighth point of the illustration of this relationship between the shepherd and the sheep is that the Jewish sheep and Gentile sheep will be brought together into one fold according to verse 16: And other sheep I have, which are not of this fold: them also I must bring, and they shall hear my voice; and they shall become one flock, one shepherd.
Previously, it was pointed out that one of the mysteries, which was contained in the New Testament but not revealed in the Old Testament, was that the composition of the Church would be of Jewish and Gentile believers united into one Body. This particular passage contains the first indication of the revelation of that mystery. The sheep about which He had been speaking up to this point were Jewish sheep. Then in verse 16, He mentioned that He had other sheep that were not of this fold. The sheep of this fold were the Jewish believers, and the other sheep were the Gentile believers, who were separated at the time John 10 was taking place. Unity between Jews and Gentiles into one flock would come only after His death, Resurrection, and Ascension. The point He made here was that both Jews and Gentiles will be brought together into one fold, the Church; they will become one flock under the one shepherd. So already as early as John 10, there was an implication that there would be a new entity of Jewish and Gentile believers.

The ninth point of the illustration is that, as the Shepherd of the sheep, He will lay down his life for the true sheep according to verses 11 and 15.
Verse 11 states: I am the good shepherd: the good shepherd lays down his life for the sheep.
Verse 15 states: even as the Father knows me, and I know the Father; and I lay down my life for the sheep. A true shepherd over his true sheep is willing to lay down his life for his sheep.

The tenth point of the illustration to be noted concerning the relationship between the shepherd and the sheep is that there are certain time-distinctions in this relationship: past, present, and future.

Insofar as the past is concerned, Jesus, the Good Shepherd, laid down His life for His sheep (Jn. 10:11).
As far as the present is concerned, He is now the Great Shepherd of the sheep and is in the process of sanctifying the sheep (Heb. 13:20-21).
Insofar as the future is concerned, the Shepherd is going to reward the sheep (I Pet. 5:1-4).

2. Five Specific Applications
The first symbolic illustration of the shepherd and the sheep has five specific applications.

The first application is that of the Messiah’s intercession: He intercedes on behalf of his sheep.

The second application is that of provision: it is not the job of the sheep to find their own pasture; it is the responsibility of the shepherd to lead the sheep to food and water. The fact that we are sheep and He is our Shepherd promises that He is going to provide for our basic needs. He does not promise to provide for our wants; that is only in accordance with His will and can differ with different believers. However, insofar as the basic necessities of life are concerned, these will be provided.

The third application is that of protection: it is also the responsibility of the shepherd to protect his sheep from attacks from the outside, be it the lion, the bear, or the wolf.

The fourth application is one of calling. At certain times of the day, the shepherd calls to the sheep with a special call that only his sheep understand and recognize. His sheep then move toward the shepherd so that they can be led to water, to pasture, or to the fold. Indeed, in this application, He is calling believers to do various functions within that fold, using their different gifts for the building up of the Body. The sheep are responsible to obey that call.

And the fifth application is one of security; there is security in this Shepherd according to John 10:27-29: My sheep hear my voice, and I know them, and they follow me: and I give unto them eternal life; and they shall never perish, and no one shall snatch them out of my hand. My Father, who has given them unto me, is greater than all; and no one is able to snatch them out of the Father’s hand.
The promise of security is that, once we become His sheep, we can never become not His sheep. Part of this relationship is the eternal security of our salvation.