Here's an approximation of current state routes (with a couple of exceptions) that get you within spitting distance of the missions, plus the four presidios and two pueblos:
-Start at Presidio Real de San Diego
-I-8 east to San Diego de Acalá
-I-8 west; I-805 north; I-5 north; CA-76 east to San Luis Rey
-I-5 north to San Juan Capistrano
-I-5 north; (former) CA-72 north; CA-19 north; I-10 west to Mission San Gabriel Arcángel
-I-10 west; US-101 north to Pueblo de Los Angeles
-US-101 north; CA-170 north; I-5 north to San Fernando Rey de España
-CA-118 west; CA-126 west; US-101 north to San Buenaventura
-US-101 north to Santa Barbara and El Presidio Real de Santa Barbara
-US-101 north; CA-154 north; CA-246 west to Santa Inés
-CA-246 west to La PurÃsima Concepción
-CA-1 north; CA-135 north; US-101 north to San Luis Obispo de Tolosa
-US-101 north to San Miguel Arcángel
-US-101 north; County Route G-18 north; County Route G-14 north to San Antonio de Padua
-County Route G-14 north; US-101 north to Nuestra Señora de la Soledad
-US-101 north; CA-68 west to San Carlos Borromeo de Carmelo and Presidio Real de San Carlos de Monterey
-CA-1 north to Santa Cruz
-CA-17 north; I-880 north to Pueblo de San José de Guadalupe
(east split)
-I-880 north; CA-262 east; I-680 north; CA-238 north to San José
(west split)
-CA-82 north to Santa Clara de AsÃs
-CA-82 north; I-280 north; US-101 north to San Francisco de AsÃs and El Presidio Real de San Francisco
-US-101 north to San Rafael Arcángel
-US-101 north; CA-37 east; CA-121 north; CA-12 west to San Francisco Solano and El Presidio de Sonoma
I used CA-72 and CA-82 even though they're not the fastest routes, but they represent former routings of US-101 (and CA-82 is called El Camino Real, after all).
If we wanted to do some real digging and get off the state highways we could come up with an even closer approximation.
I know there's one El Camino Real Bell on Main Street in Los Gatos (historical CA-17) which would correspond to this more "correct" routing. I wonder if there are others not along the "official" route?
Oops -- looks like you missed the San Juan Bautista mission, right at the north/east US 101/CA 156 interchange. That's where I got married to my 2nd wife back in 1982 (her idea!). Small as missions go, but if you're on 101, you can hardly miss it. Also: Mission San Jose de Guadalupe is actually
south of I-680 on Mission Blvd. (former CA 238, which now ends at the interchange about 3/4 mile north of the mission).
That would likely detour your mission-connecting route as follows: from Carmel, follow 1 north to 156, 156 east (partially mpxed with 101) to San Juan Bautista, then north one exit on 101 to 129, 129 back to 1 in Watsonville, then onward to Santa Cruz.