Flywheel magnets are polarized, they are opposite of each other meaning one is north and the other south...they both should strongly pull a steel bolt to them....using a magnet one should strongly attract the magnet and the other should strongly repel it. Yes they can go bad by loosing their magnetism or even reversing polarity. Typically is the second or south magnet that fails when the flywheel stops for long periods with the magnet clocked against the coil pickups or heat kills them.. With the plug out to test spark it should be very easy to archive the 250-300 rpm needed to trigger a strong spark. It sounds like you have poked at and prodded everything but the flywheel so I'd go balls deep and get a used or new oem one coming then report back to the mob on here once replaced and retested...leaving only the harness left to replace.