Jan,
Lets see what i think are your best options;
You have to do Basaseachic, Creel, and Divisadero. Depending on how many days you plan to stay in The Tarahumara, there are some other places that you should visit, we can talk about that later.
Once you get to San Rafael the best two options as you describe is to go either via Temoris-Alamos or Tubares-El Fuerte or to put it another way you go down and cross the Chinipas river without a bridge or El Fuerte River with a bridge, In May you should be able to cross the Chinipas river without a problem.
I like the Tubares route better for the sole reason that its shorter and will allow you to stay more days in the high sierra, so its really up to you. If you have some days to spare the hot ticket will be to do San Rafael-Temoris-Chinipas-San Bernardo-Alamos-El Fuerte-Los Mochis.
You are very welcome in Los Mochis and can arrange any lodging that you need (Free of course). i can also arrange a full mechanical checkdown while we go deep sea fishing

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Saludos