score:7
Short Answer: Over the course of 7 years by a committee of Apostles, Oxford Scholars, professional editors, computer experts, and many other contributers form both inside and outside the Church.
What we have for footnotes in the standard works today is the result of many lifetimes worth of diligent scripture study, and thousands of hours work completed as part of a huge effort led by the apostles Thomas S. Monson, Boyd K. Packer, and Bruce R. McConkie, Bruce R. McConkie being a very prominent contributor, having established himself as a student of scripture. In addition to writing the chapter headings, the topical guide, and the bible dictionary, he also produced many of his own footnotes (In the OT alone he produced 600 footnotes that just reference text from the JST, and produced the "Selections from the Joseph Smith Translation" for the references that were too long for the footnotes.)
The work began in 1972 with the creation of the Bible Aids committee, presided by then Elder Thomas S. Monson. The presidency of the Church wanted to publish an LDS version of the KJV Bible, previously the church had used the Oxford edition of the bible in combination with LDS lesson manuals.
The work they completed is daunting, much came from study, but a significant number of footnotes were the result of custom written programs by Stephen Howes of BYU.
Those of us who witnessed the progress of the project often commented how individuals in and out of the Church with needed skills and abilities were available at our time of need. For example, as the work progressed and it became necessary to process the manuscripts, a qualified editor, Eleanor Knowles, was available at Deseret Book. Furthermore, the project could not have been accomplished without the benefit of modern computer technology; and here again, both in the people available and in the development of technology, our needs were met. In anticipation of another project, Eldin Ricks at BYU had placed every verse of all four standard works into a computer data base. When it became desirable to have such a data base for the scriptures project, Brother Ricks willingly let the Church use his material, saving us thousands of hours.
– Wm. James Mortimer
My former Mission President, Joseph Cook–who was actually mentioned in a talk at the most recent General Conference by his brother Quentin–wrote footnotes into is journals, and would reference them while answering any questions we, his missionaries, may have during personal interviews, it was amazing. I only wish I could see Bruce R. McConkie's personal study journals, but I have a feeling that the vast majority of the fruits of his labours are currently published in the standard works as the study helps, everything else is likely contained in his book, "Mormon Doctrine".
As Brother Mortimer witnesses in the quote above, the work was nowhere short of a miracle when it came to meeting the needs of the project.
History of LDS Scriptures
Harold B. Lee Library. Bible: LDS Publication of the Bible
The Coming Forth of the LDS Editions of Scripture
Upvote:2
This is the best I could find for you. Boyd K. Packer, 1982 https://www.lds.org/general-conference/1982/10/scriptures?lang=eng
...
All of the problems mentioned so far related only to the printing part of the project. The actual compiling and organizing of the tens of thousands of footnotes would require many hundreds of workers. This work had already been underway for several years. Without the computer it would be manifestly impossible!
...
After more than seven years of quiet, intensive work, the Latter-day Saint edition of the King James Bible came off the press. Already work was well under way on the Book of Mormon, the Doctrine and Covenants, and the Pearl of Great Price. Over the years manuscripts had come into our hands which made possible the correction of printers’ errors which had crept into early editions.
Without the inspired help of hundreds of dedicated workers it would have been impossible! Among them were scholars in Hebrew, Greek, Latin, Old and New Testament studies. More than this, they are worthy men and women in whose lives the gospel of Jesus Christ is the dominating influence. Their work, if they only knew it, may well be their greatest contribution in mortality.
As the generations roll on, this will be regarded, in the perspective of history, as the crowning achievement in the administration of President Spencer W. Kimball.
There is not much more to add to this. I would suggest listening to, or reading the talk. I have only taken bits and pieces out of it.
So to answer your question. Yes. It was a manual process and a computer process.