I've got the identical problem with the same year and hp merc. It's a 25 XD. Had weak spark on the top cylinder, replaced both coils. Got strong spark on both cyl's but no combustion on top cyl at idle. Trigger was broke on it's mount and replaced it. Still no combustion fire at idle on top. Thought maybe the trigger damaged the switch box, I heard that possibilty somewhere, so replaced the switch box.
In testing everything, the trigger that should only put out about .5 V is putting out 11 to 13 V and testing both trigger wires, the test on the other wire will kill the engine. Ohm testing the stator shows totally backwards. Black/yellow wire that should have 3300 to 3800 ohms is showing very little and black/white wire is also not up to specs but closer to specs. All this with great spark at idle, but the top plug stays clean and shows no combustion firing. Voltage out of the pack to the coils is in specs, and firing on time. New plugs, and wires.
I'm going to pull the lower unit and run without water to be sure the top cyl, isn't getting water intrusion from somewhere. If it fires on top then, it could be water getting in somwhere to the top. if it still doesn't fire in the cyl then, i'm going for the stator replacement. I won't be running it hot, just long enough to check if it combusts when no water is circulated.
I've checked everything I know to test, even replaced the exhaust cover gaskets, and sprayed around the engine with carb cleaner, checking for air leaks. Yup, the carb got cleaned first thing.
I'll get back after some further investigations.