I finally mustered enough courage to climb up on the roof today. It was not at all a pleasant experience. The metal is slippery enough by itself, and the blanket of pine needles made things even more exciting. Even so, I survived without injury.
I understood why it was leaking as soon as I got up there. The boot for the chimney was installed with the flashing on top of the metal roof material all the way around. A pitiful attempt to seal the top edge was made with some kind of clear sealant that was both poorly applied, and already degraded, despite being in place for less than a year. The sides were left completely unsealed.
I coated the entire area with Leak Stopper – top surface where the boot mates to the chimney, side seam, and all the way around the flashing. I tried to avoid creating any new valleys, and did my best to adequately cover everything without going overboard.
Although there is light rain in the area now, I will not know whether or not my repair was a success until the next extended downpour. I feel pretty confident, though. I’ll have to reapply every few years, perhaps more frequently, but I will be surprised if any water penetrates before 2015.