To properly answer this question depends on the answer to
some other questions:
1. Do you want to see all the missions in a "grand tour" or break the visit into segments?
2. To what extent, if any, do you want to see other mission-era sights? Asistencia (sub-missions), mission era buildings, museums etc.
3. Related to point #2, how much time can you allocate? (For example, It is possible to see the three most southern missions (San Diego, San Luis Rey and San Juan Capistrano) in two days. However there are other mission era sights that could extend the time. In San Diego alone there is Old Town San Diego - which has several important mission era structures, the Cabrillo Monument, the Serra Museum on Presidio Hill and the remnants of the water system near the mission...not to mention the San Antonio de Pala asistencia (sub-mission) about 30 miles east of San Luis Rey.
For example, if you were to plan an eight day + trip that only allowed time for visits to the missions and a few nearby mission era sights, this preliminary itinerary could be helpful:
Drive to Sonoma the night before and start with Mission San Francisco Solano. Be sure to see the site of the Bear Flag Revolt on the square and the Soldiers Barracks. If you have time drive to General Mariano Vallejo’s house on the outskirts of town (2-3 hours).
Drive to San Rafael and see the mission replica. (1- hour).
End the day visiting San Francisco de Asis in downtown San Francisco. Be sure to visit the cemetery. (1-2 hours)
Consider driving that evening to Fremont, for an early start the next day.
Visit Mission San Jose. (1-2 hours)
Drive to Santa Clara University and visit historic Mission Santa Clara on the grounds of the school. Be sure to look at the rose garden (the former cemetery) and the ruins of the old walls that are preserved (1-2 hours)
End the day with a visit to Mission Santa Cruz. Be sure to visit the nearby Mission Santa Cruz State Historic Park where there is an authentic mission era adobe (former Indian housing).
At the end of the day drive to the town of San Juan Bautista, which is quite charming, so you can get an early start the
Spend as much time as you can at the San Juan Bautista mission and the adjacent state park. This contains the only authentic Spanish era plaza and some 20 historic buildings (2-3 hours)
Drive to Carmel and visit Mission San Carlos Borremeo de Carmelo. This is a beautiful mission with wonderful grounds, a great museum and plenty to see (2-3 hours)
If you had another day I would spend it here and visit Old Monterey.
Make your way to Route 101 going south. Stop and see Mission Soledad (1 hour).
Drive from Soledad to San Antonio de Padua. Allow enough time to get thru the check points on the military reservation that surrounds the mission. San Antonio de Padua will be one of the highlights of your trip. This wonderfully restored mission has a great church, an interesting museum, a full quadrangle, several important exterior delays and ample grounds (well marked with signs of what present in the mission era). (2-3 hours).
Consider staying at the hotel on near the mission.
Touring San Miguel will not take as much time as we would normally recommend because the church was badly damaged in an earthquake in December, 2003 and much of the mission is closed. (1 hour)
San Luis Obispo. This is an interesting mission in an interesting town and we would normally recommend you stay here but your time is limited. Visit the church, walk the grounds and be sure to spend time in the museum (1-2 hours)
La Purisima, in Solvang, will take 2-3 hours to see and you could easily spend more time as this mission was fully restored in 1930s and contains over twenty buildings.
We recommend driving to Solvang to be positioned to cover a lot of ground the next day.
Visit Santa Ines before it opens, to take photographs of the mission as the sun rises. This is a wonderful mission with well preserved grounds and a lot to see. (1-2 hours)
Then, drive to Mission Santa Barbara to see the mission which has an excellent museum and lovely grounds. (1-2 hours) Ordinarily we would recommend more time and a visit to the partially restored Santa Barbara Presidio but you are not likely to have enough time.
Drive down the coast and stop in Ventura to visit San Buenaventura. (1 + hours). The interior of the mission church has been nicely restored and there is a small museum and displays on the grounds.
To save time the next day, drive to Los Angeles and stay near Mission Hills.
San Fernando Rey is a big complex that will take time to see properly but if you want to complete your trip in eight days you will have to hit the highlights: the Convento, or Long House, the museum and the church interior. (1-2 hours)
Mid morning head for the town and mission of San Gabriel. This is an impressive fortress like church with a well organized tour. Again you may be pressed to do it justice (1-2 hours)
In the early afternoon go south into Orange County to the town and mission of San Juan Capistrano (2-3 hours). This mission contains the original Serra Chapel, spell binding ruins, extensive displays and lovely gardens. Spend as much time there as you can.
We recommend staying in San Juan Capistrano and getting up at the crack of dawn to try to beat the morning commuter traffic to get to Oceanside.
Visit San Luis Rey (1-2 hours) and then decide whether you want to see the San Antonio de Pala Asistencia, some 30 miles east of San Luis Rey (1-2 hours) or you would rather spend more time in San Diego.
Drive to Mission San Diego mid day and tour this inspiring mission (1-2 hours). You could easily spend more time.
As we discussed while you are in San Diego visit the Serra museum on Presidio hill, the original site of the first mission and presidio in California.
Some additional tips:
1. Spend some time viewing each mission on the computer, via the Visual Journeys we have posted on our website. You may have to make some tough trade-offs. Be prepared to adjust the amount of time you spend at each mission and be prepared to be disappointed in a few.
2. Do plenty of reading beforehand. That will not only enhance the quality of the experience it will help you plan photographs and have a checklist of what you want to see.
3. To the extent possible time your visits to avoid certain events including fund raisers, festivals (so crowded you can't see anything), peak school days. Go in good weather (f there ever will be such again in California.