I would think that our preparation for kabbalas hatorah (shavuous and omer) would be a happy time, yet it is dominated by the mourning of the sefira period. How do we reconcile these?

Shalom, Thank you for your question. You have hit on an important point here. The days leading up to the festival of Shavu'ot are certainly supposed to be filled with joy. In fact the Ramban writes that they are like one long intermediary days (chol ha'moed). The festival of Passover stretching out up until Shavu'ot. Also in kabbalistic thought this are special happy days. On the other hand we do have a measure of mourning during these days to recall the death of Rabbi Akiva's students. I quote from an article by Rav Melamed from our website – " The Reason for Mourning During the Omer - The days between Passover and Shavuot are marked by pain, for during this period twenty-four thousand of Rabbi Akiva’s students died. For this reason, the custom is to observe mourning practices during these weeks - weddings, haircuts, and dancing are all forbidden. Before addressing the details of these mourning customs, it is worth expanding a bit upon the core of the matter: the reason for the deaths of Rabbi Akiva’s students. The Talmud states: "Rabbi Akiva had twenty-four thousand students and all of them died in one period of time because they did not treat each other with respect. It is taught that they all died between Passover and Shavuot, and that they all suffered bitter deaths" (Yevamot 62b). Another source informs us that after this tragedy Rabbi Akiva raised up additional students, and he said to them, "All of my former students died because they looked jealously upon one another. Make sure not to do as they did.." Since then, the days of the Omer counting are observed as days of semi-mourning, a period wherein we attempt to improve relations with others. I heard an interesting explanation of the reason behind the deaths of Rabbi Akiva’s students. It goes as follows: The plague which took the lives of Rabbi Akiva’s students concurred with the Bar Kochba uprising. Some of Rabbi Akiva’s students joined the rebellion while others continued in their studies.. The two camps behaved contemptuously toward one another. Each claimed to be greater than the other, boasting that its behavior was more important and effective and that that of the other was of no benefit. Because of this groundless hatred between soldiers and students all of them were stuck down before the enemy.. Indeed, the date is not coincidental. It falls between the Passover Festival on the one hand, which represents Israel’s national aspirations, and Shavuot on the other, which represents the giving of God’s spiritual Torah. By not respecting each other the students of Rabbi Akiva in effect drove a wedge between Passover and Shavuot, between national aspiration and Torah, and therefore they all died during this period. Some thousand years later, with the onset of the Crusades, Christians killed tens of thousands of Jews. These tragedies also took place for the most part during the Omer counting period. And again, some five hundred years later, an additional slaughter of Jews took place - this time in eastern Europe - which claimed the lives of tens, if not hundreds of thousands of innocent Jews. The latter massacres too took place during the days of the Omer. For this reason, Ashkenazi Jews have customarily been more stringent about mourning during this period." So, we have two contradictory approaches to these days – happiness and sadness. In truth the underlying holiness of these days is connected to joy. However, because of some tragic historical events that inner joy is covered over with a level of mourning. Through our efforts to improve ourselves, and as the Jewish people return to their true essence in their land, we will slowly but surely uncover the true holiness and joy of these days. In fact, I heard that it is not by chance that the two modern festivals of Yom Ha'Atzmaut (Israel Independence Day) and Jerusalem Day both fall out during the Omer days. This is a testament to the gradual process of spiritual and physical redemption we are going through. May we merit to be part of the complete redemption speedily in our days.