I suspect there are two possible reasons for the problem with initial conditions. Is this a network drive that perhaps has restricted permissions and is not allowing SyncroSim to create a folder here? It is also possible that the path is too long. I would try to put your library in a different location.
You are right about there being no fixed rule for determining transition probabilities. The method you use will depend on the questions and model, as well as on the available data. I recommend you read through some of the published examples (https://docs.stsim.net/publications.html) to see the different approaches people have taken.