you already have the unit so I would step back and take a good look at what it needs and what you time and abilities are. from a reply above it sounds like you may have over paid so you will probably take a substantial hit if you sell it now.
Are there any soft spots in the roof near the stains? or on the floor where it may have came done? if everything seems solid I wouldn't worry about the stains. soft spots could be major.
did you prep the roof properly before applying the EDPM coating? apply 2 coats? A tear in the roof is easy to fix with externabond tape.
being able to do most of your own work is a major plus as they will always need work as they are typically not the best quality and need to be light weight and bounce done the road
