I went to the temple today specifically looking for references to Christ in the endowment. It yielded a rich harvest that warrants much further investigation. Not even counting every individual reference to Him, there were some pretty significant things I noticed.
The first and last words in the endowment are clear references to the Savior. Truly, He is Alpha and Omega: even in the temple, Jesus Christ is the beginning and ending of everything. Literally.
More fascinating still were the major references to the Atonement itself. I counted five. (I’d love to attend a session of work there with you sometime and discuss in more detail where I saw these five references and the insightful language the endowment uses to describe it!)
Of course, this is perfectly natural. The largest overarching theme of the endowment is the physical and spiritual reconciliation of mankind to God through Christ. In fact, viewed in that vein, the entire endowment itself could be seen as a symbol of the Atonement.