the described behaviour can be characteristic of an overheating coil. basics checks of the resistance of the coil's windings (as per the video) are a good start and will quickly identify a dead one. intermittent issues are of course harder to track down.
it is worth also checking the other parts on the secondary side of the coil, so any HT leads etc. (i'm not familiar with the ignition system on the bonneville) and the condition of the spark plugs. a heavily fouled/intermittently firing plug, or a high-resistance connection somewhere can create an over-voltage condition in the coil which, over time, could damage the insulation of the windings. it could be that in your case the insulation was deteriorating due to that (or age) and a period of idling caused an excessive build up of heat that has finally caused something to fail.
say, for example, it has caused a crack in the insulation of the secondary winding. it may well be that when cold the crack is closed or so narrow that resistance measurements look fine, and the engine can operate normally.
in operation the coil will heat up and the winding wire will expand, causing the crack to start to open. if you start to get arcing at this point in the circuit then clearly that is lost power that never reaches the spark plug, so you get a weaker spark.
a weaker spark does not necessarily mean the engine will immediately stop. when cruising at moderate revs the conditions within the combustion chamber are (crudely, without getting into details) more conducive to the creation of a spark, so a reduced voltage at the plug will still create a good enough spark for combustion. in this scenario the problem would most likely manifest when you idle or run at low revs.
as WR suggests it's difficult to test without having some known good coils, in which case you've likely already spent some money :S
