I'm sorry, I don't have a solution for you but I am guessing that because permissions relates to 'roles' (and not groups or cohorts) that it is not currently possible to have an activity/resource visible to only one group.
Thinking creatively, I guess you could do it via creating a conditional activity for each resource and then only showing the document if they have a required grade on the other activity. Then giving each student in each cohort / group an appropriate grade in the appropriate resource would work for it. In fact, you could do it by just having 1 dummy activity which you grade, giving all students in one cohort 25%, and the others 75%. Then add conditional activities to the two resources to be 'above 50%' for one, and 'below 50%' for the other. If you think they might be concerned about getting a 25% I guess you could do it much higher (eg. 99% and 97%??). I haven't tried this, but I don't see why it wouldn't work.
Having said that I think it could be something worth considering for the future direction of Moodle, so perhaps see if a feature request has been made and if not, suggest it.