..........You should never pour mineral spirits , acetone , lacquer thinner , etc. directly onto a Rubber Roof(EPDM)! Doing so will dissolve the rubber roof as well as the glue that attaches it to plywood underneath . You will end up with a Bubble and potential problems down the road ! Mineral spirits is a very good cleaner , BUT it should be poured on a rag , and IF the roof is rubbed too hard it can still cause the roof to come lose from the plywood . I would use some kind of mild soap rather than MS's .
...........You should clean the area around the leak then apply a length of Eternabond to fix the leak . Eternabond can be applied over existing caulk if the lose caulk has been removed . , jf