Roof Armor will be $4K+, they do a nice job but if you look at the steps it's very labor intensive. You can get Heng's Roof Coating and roll it on for $50/gal, but that's just another layer of EDPM...usually the rubber membrane itself is not what's leaking unless it has had puncture damage from a tree limb, etc. Usually the leaks are at seal points like vents, TV antenna, etc. You're not seeing drips inside because the water is being absorbed by the flakeboard roof sheathing and insulation. When it gets saturated, it will drip down a wall and start to rot the floor.
I think the plan you have now is best to get you through the winter, and is what I was going to suggest. You really have to play detective, find out what's leaking, where the water is coming in and how extensive the damage is before you formulate a plan to fix it. Usually you only see about 10% of the damage, so figure that soft spot where there's nothing behind the rubber roof is about 1/10 of what needs to be fixed.
