There are a lot of SabMag posts related to ignition problems. The troubleshooting guide in the Honda manual is OK, but it doesn't explain how the system works. The following simplified explanation is adapted from Tranter.
The SabMag ignition system is frequently referred to as a capacitor discharge (CDI) system, but it is actually a more advanced transistorized system. Basically, there are two separate systems, one for cylinders 1 & 3 and one for cylinders 2 & 4, as diagrammed in the manual, with the major components of each being the pulse generator, spark unit, and ignition coil. Base timing is determined by the position of a protrusion on the starter clutch. (In the Honda manual for the V65 Magna, you can see it in the drawing at the top of p. 7-13 and under the left index finger in the top photo on p. 7-23.)
The protrustion acts as a "reluctor." That is, when it approaches the pulse generator, which is a coil with a magnetic core, it induces a change in the field of the magnet that in turn induces a voltage pulse in the coil. A second pulse is generated as the protrusion leaves the pulse generator. Since the generation of these pulses is strongly dependent on the distance between the reluctor and the magnet, the air gap between the protrusion and the pulse generator must be correct.
In the spark unit, the "pulse shaper" adjusts the voltage signals from the pulse generator to give a clean cutoff of current to the primary side of the coils and to compensate for variations in pulse voltage due to engine speed. The spark unit also controls advance and dwell, amplifies primary voltage to the coils, and adjusts for variations in battery and alternator voltage. Their complexity and construction are why it is not practical to test or repair them. They either work or they don't. (Many would disagree with this statement) The 1-3 unit controls the tach, so a sudden loss of power and a failed or screwy-acting tach indicates a failed 1-3 spark unit. From the spark units to the plugs, the system is pretty conventional, except that each subsystem fires both plugs every revolution. That is, each plug fires at the top of the exhaust stroke as well as at the top of the compression stroke.
We have one report of a coil that tested good according to the tests in the Honda manual, but which tested bad at the dealer's shop. Thus, if you're having problems with firing on the 1-3 or 2-4 cylinder pair, and it isn't the spark unit, you might want to have the coil tested by the dealer or an electrical shop.
You may have to fabricate/change the mounting:Accel 140403 Dyna DC1-1 (flip the bracket for the V65 Magna)
Aftermarket Plug Wires & Caps
(Solid copper core plug wires - 7mm)
Accel (yellow and blue color available)
NGK 5K ohm spark caps