Both branches were cut off from the root, but Ephraim has been grafted back in as the Church. Judah still lingers, but is provoked to jealousy by Ephraim's praise and worship, and God clearly indicates that ALL Israel will be saved. More Messianic Jews are appearing these last days and recognizing Messiah Yeshua. This is stated in Ez.37:11-17 to happen and repeated in the New Teastament many times or referred to. I just bumped into another reference recently:
Hebrews 8:7 For if that first covenant had been faultless, then should no place have been sought for the second. 8 For finding fault with them, he saith, Behold, the days come, saith the Lord, when I will make a new covenant with the house of Israel and with the house of Judah:
Acts 13:23  Of this man’s seed hath God according to his promise raised unto Israel a Saviour, Jesus:

If the unbelieving Jews were objects of wrath prepared for destruction before the foundation of the world, then why did Paul say they did not stumble beyond recovery?

The last part of your question is explained later on in Romans to some degree.
Romans 11:25  For I would not, brethren, that ye should be ignorant of this mystery, lest ye should be wise in your own conceits; that blindness in part is happened to Israel, until the fulness of the Gentiles be come in.
26  And so all Israel shall be saved: as it is written, There shall come out of Sion the Deliverer, and shall turn away ungodliness from Jacob:
27  For this is my covenant unto them, when I shall take away their sins.
28  As concerning the gospel, they are enemies for your sakes: but as touching the election, they are beloved for the fathers’ sakes.
29  For the gifts and calling of God are without repentance.

I believe the Bible indicates that ALL of Israel will be saved. This includes the house of Judah (the Jews) in Israel at this present day. The Gentiles, which include all the grafted in branches and the house of Ephraim, are being gathered now and provoking the Jews in Israel to jealousy. The Jewish people watch closely and see the celebration of those in Christ even now and this makes them wonder.
God's gifts and calling are forever, and none of His chosen will be lost, but redeemed. I know there are many different views on end times and the Jews in Israel, but through out the Bible God redeems both houses of Israel - Ephraim and Judah. This, and all the grafted in branches. Go back and read all the curses and trouble prophesied to the individual houses and they are different to some extent as He addresses them indiviually, yet God always ends the trouble with salvation and redeemption. Hosea is a good example to read.

Hosea 6: ¶ O Ephraim, what shall I do unto thee? O Judah, what shall I do unto thee? for your goodness is as a morning cloud, and as the early dew it goeth away.
5  Therefore have I hewed them by the prophets; I have slain them by the words of my mouth: and thy judgments are as the light that goeth forth.
6  For I desired mercy, and not sacrifice; and the knowledge of God more than burnt offerings.

Hosea 11:9  I will not execute the fierceness of mine anger, I will not return to destroy Ephraim: for I am God, and not man; the Holy One in the midst of thee: and I will not enter into the city.
10  They shall walk after the LORD: he shall roar like a lion: when he shall roar, then the children shall tremble from the west.

Interesting that we, in America are considered the west.

Ofcourse it is God's call, but scripture also says that to whom much is given much is expected. Everyman is judged according to what God has given him, so, indeed, God knows this amount and is able to judge much better than man.

Here is a good link with day by day explanation of events leading to the Lord's resurrection:
http://centuryone.com/crucifixion.html