As I understand it the only definitive diagnosis is PM I am afraid. The next most reliable method is by faecal PCR test and also blood tests can be done. One suggestion, cost permitting is getting them all faecal and blood tested. As I understand the are first and foremost pets depending on what the results are and what your vet recommends you there are ways that Johnes can be "managed" / contained and (hopefully) eradicated from the herd involving splitting of positive and negative animals, 6 monthly testing, "snatching" animals at birth and artificially rearing, management of buildings and land as Johnes can be persistent in the environment (faeces?) for 12 months I believe. I read something about this in managing Johnes in a commercial beef herd using these techniques in an ADAS bulletin and they may be safely adaptable to your setup following guidance from your vet As you say a vaccine is available so is worth looking into. Good luck!