What is Reasoning behind the Inquisition and Separation of Holy days to be separate from the Israeli Sabbath

With respect to the Inquisition: the Catholic Church has long recognized this as an evil done by the Church of past years, and has repented and asked God for forgiveness:

The institution of the Inquisition has been abolished. ... The children of the Church cannot but return with a spirit of repentance to "the acquiescence given, especially in certain centuries, to intolerance and even the use of violence in the service of the truth" ("Address to the International Symposium on the Inquisition Organized by the Central Committee for the Great Jubilee of the Year 2000", 31 October 1998, n. 4; L'Osservatore Romano English edition, [ORE], 11 November 1998, p. 3).

This spirit of repentance, it is clear, entails a firm determination to seek in the future ways to bear witness to the truth that are in keeping with the Gospel.

On 12 March 2000, on the occasion of the liturgical celebration that marked the Day of Pardon, forgiveness was asked for errors committed in the service of the truth by recourse to methods not in keeping with the Gospel. The Church must carry out this service in imitation of her Lord, meek and humble of heart. The prayer I addressed to God on that occasion contains the reasons for a request for forgiveness that can also be applied to the tragedies associated with the Inquisition, as well as to the injuries to memory that result from it.

"Lord, God of all men and women,
in certain periods of history
Christians have at times given in to [forms of] intolerance
and have not been faithful to the great commandment of love,
sullying in this way the face of the Church, your Spouse.

Have mercy on your sinful children
and accept our resolve
to seek and promote truth in
the gentleness of charity,
in the firm knowledge that truth
can prevail only in virtue of truth itself.
We ask this through Christ Our Lord."

(Letter of John Paul II to Cardinal Roger Etchegaray on the occasion of the presentation of the volume "L'Inquisizione", 15 June 2004)

The Church rejects what it has done, in the understanding that the Holy Spirit has led it to a new interpretation of how to bring others to the knowledge of God.

Similarly, the Church recognizes that some of its actions and attitudes with respect to Jews were not in keeping with the commandment to "love your neighbor". This attitude, too, has been rejected:

True, the Jewish authorities and those who followed their lead pressed for the death of Christ; still, what happened in His passion cannot be charged against all the Jews, without distinction, then alive, nor against the Jews of today. Although the Church is the new people of God, the Jews should not be presented as rejected or accursed by God, as if this followed from the Holy Scriptures. All should see to it, then, that in catechetical work or in the preaching of the word of God they do not teach anything that does not conform to the truth of the Gospel and the spirit of Christ.

Furthermore, in her rejection of every persecution against any man, the Church, mindful of the patrimony she shares with the Jews and moved not by political reasons but by the Gospel's spiritual love, decries hatred, persecutions, displays of anti-Semitism, directed against Jews at any time and by anyone.

(Nostra Aetate, "Declaration on the Relation of the Church to Non-Christian Religions", October 28, 1965)

Finally, with respect to your comments on the Sabbath: The Church teaches that the Sunday observance is in fact distinct from the Sabbath, and replaces the Jewish Sabbath observance:

Sunday is expressly distinguished from the sabbath which it follows chronologically every week; for Christians its ceremonial observance replaces that of the sabbath. In Christ’s Passover, Sunday fulfills the spiritual truth of the Jewish sabbath and announces man’s eternal rest in God. For worship under the Law prepared for the mystery of Christ, and what was done there prefigured some aspects of Christ:

Those who lived according to the old order of things have come to a new hope, no longer keeping the sabbath, but the Lord’s Day, in which our life is blessed by him and by his death. [St. Ignatius of Antioch, Epistula ad Magnesios (Letter to the Magnesians)]

The celebration of Sunday observes the moral commandment inscribed by nature in the human heart to render to God an outward, visible, public, and regular worship "as a sign of his universal beneficence to all." Sunday worship fulfills the moral command of the Old Covenant, taking up its rhythm and spirit in the weekly celebration of the Creator and Redeemer of his people.

(Catechism of the Catholic Church, paragraphs 2175–6; emphasis added)