While Nichiren Daishonin emphasized the importance of daily reciting the "Expedient Means" and "Life Span" chapters, he never mentioned a specific format. Over the centuries, the format of gongyo has changed several times. As Nichiren states, "Though no chapter of the Lotus Sutra is negligible, among the entire twenty-eight chapters, the "Expedient Means" chapter and the "Life Span" chapter are particularly outstanding. The remaining chapters are all in a sense the branches and leaves of these two chapters. Therefore, for your regular recitation, I recommend that you practice reading the prose sections of the "Expedient Means" and "Life Span" chapters." ("The Recitation of the 'Expedient Means' and 'Life Span' Chapters, "The Writings of Nichiren Daishonin, vol 1. p. 71)
During the time of Nichiren Daishonin and Nikko
The only thing clear about the form of gongyo in the days of Nichiren and Nikko is that it consisted of the "Expedient Means" and "Life Span" chapters. This can be ascertained from reading the Writings of Nichiren Daishonin "Recitation of the 'Expedient Means' and 'Life Span' Chapters" (The Writings of Nichiren Daishonin, vol. 1, p 68-72). The recitation of the "Expedient Means" chapter did not stop with the "ten factors" (the lines that are repeated three times, ending in honmak kukyo-to) as it does today; it included the longer verse portion that followed.
In addition, a phrase from the "Understanding the Meaning of the Object of Devotion for Observing One's Mind" The Writings of Nichiren Daishonin Vol. 2, p. 604) refers to Nichiren's "morning and evening practice of the Law." This indicates Nichiren did gongyo morning and evening while at Mount Minobu. It is not clear whether Nichiren practiced gongyo at other times, or at what specific time of day.
In "The One Essential Phrase" Nichiren Daishonin explains the great power and benefit of the primary practice of chanting Nam-myoho-renge-kyo. In other works where he elucidates his teachings, he explains the importance of reciting portions of the "Expedient Means" and "Life Span" chapters of the Lotus Sutra. Together, chanting Nam-myoho-renge-kyo and reciting portions of the Lotus Sutra comprise the primary and supplementary components of daily practice before the object of devotion, the Gohonzon. "The Lotus Sutra represents the bone and marrow of all the sacred teachings of the Buddha's lifetime, and the verse section of the 'Life Span' chapter represents the soul of the twenty-eight chapters of the sutra. The various Buddhas of the three existences look upon the 'Life Span' chapter as their very life, and the bodhisattvas of the ten directions likewise regard the chapter's verse section as their eyes." ("Letter to Horen," WND, 516)
Nikko, too, it seems, recited from the "Expedient Means" and "Life Span" chapters ("On the Betrayal of the Five Senior Priests," [Gosho Zenshu, p. 1616]). Another reference to gongyo is in Nikko's transfer document to his successor, Nichimoku, titled "On Articles Bequested by Nikko." He states, "Nichimoku will be responsible for administrating and maintaining Taiseki-ji and sites on its grounds such as the main temple and our master's tomb and should perform gongyo at those sites with the expectation for kosen-rufu." From this we can see that gongyo was conducted at places like the main temple and the Daishonin's tomb.
"In light of all this, we can say that each morning, [when he recites the verse section of the 'Life Span' chapter] the priest Horen is sending forth golden-hued characters from his mouth. These characters are 510 in number, and each character changes into a sun, and each sun changes into a Thus Come One Shakyamuni. They emit great beams of light that penetrate the earth and shine upon the three evil paths and the great citadel of the hell of incessant suffering." ("Letter to Horen," WND, 517–18)
More details on the practice of gongyo.