A lot of the Mission's graffiti seems to have been inscribed after the end of the mission system, but before Charles Fletcher Lummis' Landmarks Club started taking the first steps toward preservation.
That said, it wasn't uncommon, even during the earliest days of the Missions, for neophytes (Indians converted to Catholicism) to carve graffiti into the church walls. Those soft white walls seem to have invited vandalism from the beginning. That said, I think the "Nacho 1796" inscription in the photo above (by Sylvia A. of Laguna Beach) looks like a fake, as does an obvious gag where someone carved "Joaquin Murrieta 1865."
Other photos found online show graffiti at the Mission reading "“RP, Apr. 12, 1898,” (on the arm of a still-used bench), and an 1825 inscription of the names “A. Richardson" and "A. Salas.”
The photo above was taken in the early 1900s and shows graffiti on one of the Mission’s walls reading, "D.J. Hayman," " F.A. Birro," "A.W. Collum," "C.R. Moore," "A. Roe," and "Esstamapaucho July 5 1903."
Of those, I was only able to get any traction on Collum. In 1909 A.W. Collum of El Toro (now Lake Forest) ran an ad in the Los Angeles Times, reading, "For Sale - In a good, little country town on the Santa Fe Railroad. One-chair barber shop with one pool table, good cigar tobacco and soft-drink trade; only place of the kind here; large building with extra living rooms, garden, and room for chickens; free water; rent only $10. Fine place for barber with family. Reason for selling, I am alone and not a barber; will sell very cheap if taken by July 1. Better come quick for a bargain."
Two years later he had left the bucolic charm of El Toro behind and was selling brooms in L.A. Serves him right for defacing a church!
Also appearing in the photo above, and scrawled over the date “[19]01," were "J. Salaberri," "F.A. Salaberri," "G.L. Johnson," "J.B. Pitblado."
It didn't take much digging to find that Juanita Salaberri (1879-1964) was one of the daughters of Juan Salaberri, one of Capistrano’s wealthiest men. Don Juan raised sheep and had a hotel and a general store in town. He came to Capistrano about 1873, and died there in 1898.
“F.A.” was Juanita's sister, Felicitas "Felley" Salaberri (1881-1960).
And James Bruce Pitblado (1875-1934) was presumably Felley's boyfriend, because he went on to marry her in 1905.
In the photo of the Mission's Bell Wall, below, (courtesy the San Juan Capistrano Historical Society), Juanita appears on the far right, and Felley on the far left. (Had the photographer gotten there just seconds earlier, he no doubt would have caught the sisters in the act of vandalizing the building!) Standing between them are Lucana Forster McFadden and Ysidora Forster Echenique -- cousins of the Salaberri girls.
All this makes me want to go back to the Mission on a quieter day and see what other old graffiti I can find. Meanwhile, try your hand at deciphering these names from inside a niche in the Great Stone Church.