From Santa Cruz we took the 11 o'clock flota (big bus) from terminal bimodal to San José. On thursdays there is also a train service for this route. In San José I can recommand to stay at the hotel Las Charapas a bit outside the center, which is run by Johan who is super nice and caring for his guests. Also the place is beautifully clean with a pool behind which a lot of tucans are living in this time of the year. We got a double room for 235 BOB a night. At the church next to the big plaza in San José we met Oseas after the service who was educated as priest but now is the gatekeeper of the church. He happily shows you around the church if you ask for him. We checked out the museum the next day, which has material for at least 5 hours to read through if your Spanish isn't so good but it's hard to filter out the interesting bits. It's hosted in the Colegio next to the church. The church itself is the only stone church of the WHS- the others are made of wood. The material was available from a nearby hill. At night the church is beautifully illuminated.   
 
A tip outside the WHS scope follows. At Johan's place we met Peter Neufeld who lives in Campo 26 in the huge Mennonite colony Nueva Esperanza on the way between San José and San Rafael. On wednesdays he's in San José to sell food from his farm in town and also to the hotel. We approached him and arranged a 2 night stay on his farm inside the Mennonite colony. It was a fascinating experience for us and for them to understand the different lifestyles (and for them to check out our smartphones). I can recommand it even though it's very untouristy (yet) and was more a bilateral agreement. A taxi driver took us to the farm aside kilometer 41 for 130 BOB and a Trufi (Mini Van) picked us up two days later at the same spot after the colonists brought us back by carriage to the main road.  
 
In San Rafael we arrived at 12:45 p.m. with the 09:30 Trufi from San José. As the connecting Trufi to San Miguel was already due 15 minutes later we decided to take a later one at 5 p.m. i can not confirm that this passage is only possible by mototaxi as Patrik wrote which would have been impossible and expensive with our luggage, the road and the darkness after 6 p.m.. However the rest of Patrik's review helped us a lot :). For us also the San Rafael church was open and no one was there so we could stroll around. From the outside it's beautiful. The inside is dirty and looks like further renovation is needed. The climb up to the bell tower made us think that this wooden structure could collapse any time and it should be rather locked. Afterwards we had a coffee until the trufi started at the terminal. 
 
In San Miguel we slept that evening super cheap in Hotel Limbania close to the plaza. We could visit the church just before the service. The next morning it was also open before the trufi got us to San Ignacio, which is a bigger pleasant town. I liked the paintings on the wall in San Miguel even though similar to the other churches later.  
 
From San Ignacio we took the only (!) Trufi to Santa Ana at 10:30 a.m.. We waited two hours at the terminal in San Ignacio which is way too far outside town as the receptionists of our hotel told us there are only trufis in the early morning to Santa Ana. That was wrong. The return Trufi from the village is at 1:30 p.m. When we arrived the woman said there is no space in the return trufi and we were a bit shocked especially because we couldn't reserve it anyway before going to Santa Ana. But the driver of our trufi stressed the importance that we need to get back later that day to our hotel and somehow the woman arranged us two seats in the return trufi two hours later. The church is the smallest from the six. Thanks Patrik for the tip with the tourist info at the plaza. She gave us a 15 minute tour through the otherwise closed church during the lunchbreak. Afterwards we visited (and found) the Viborón, a huge stone snake apparently made by indigenous people a long time ago and now restored. In San Ignacio I can recommand to check out the Casa de la Cultura for semi- self- organized trips to PN Noel Kempff Mercado. Currently it's not recommanded to go as the whole park is red danger zone for drug criminality but if you want to cheaply visit it these people in the tourist office are really helpful. 
 
The trufi from San Ignacio to Concepción takes two and a half hours on a nicely paved road. All other roads from San José to San Ignacio are currently and since years a catastrophe. I can not recommand to travel it at nighttime as even during daytime some drivers couldn't distinguish between locked construction site and the part of the dirt through which one should drive. In the future everything except the way to Santa Ana should be paved. The Concepción church surprised us with really modern paintings showing the crucification. Impressive are also the individually carved benches with distinctive motives on each side. There is a mission museum and by entering it you can also access the cathedral museum and the church itself. The mission museum hosts many artefacts from the history of the church without many explainations. I liked the miniature model of a Chiquitania Jesuit mission with labels. There is also a room on Hans Roth who lead the restoration of the churched. The cathedral museum has some pictures of the restauration and some Spanish texts on the history. It's worth a 2 hour visit I would say.  
 
The drive to San Javier was terrific as the driver tended to drive on the left and not on the correct right side of the street even if there were in parts no potholes on our side and even in curves where he couldn't see. The other trufi passengers were of the opinion that god would protect them but we rather asked the driver several times to stay on the right from the seats at the rear of the car. We left our luggage in the trufi office of San Javier and walked two blocks to the church. It was Sunday at lunch time and it was closed. However walking around the building along the closed museum we found an open driveway into the backyard of the church. We walked past some people that didn't care and by this we were able to visit the beautiful indeed quite white interior of the church. It contains the supposingly official UNESCO certificate and altar paintings that show the process of christianizing the indigenous people and even a black person. In the garden lives an enclosed ñandu. 
 
All in all I liked to travel the towns in Chiquitania. The weather is pleasant, there are good hotels for good prices and the churches (and the plazas) give the otherwise boring towns some flair. I found that the churches were all quite similar and it's also sufficient to visit only one of two of them. But if you have time why not visit them all? I also watched the Hollywood movie "The mission" which helps a bit to grasp an idea of how life could have looked like back in the Jesuit days. Otherwise I find the churches not so lively to tell the story. Also the few museums don't really give you a feeling about what things were like but only extend the exhibited materials.