OK, well what are you using for a key switch, or stop switch? There are several types of stop/kill switches available, some use an external ground while others do not. Shutting off your engine is accomplished by connecting the two primary circuits together, not by adding an auxiliary ground to shut the engine off. So, using some stop/kill switches that rely on an auxiliary ground might explain why just one cylinder is losing spark when the key/stop/kill switch is turned "off".
It is also important to mention that all engine functions be wired separately from boat wiring such as lights/bilge pump. Wiring lights/accessories into one of the "m" terminals on the key switch is a big mistake because a coil primary winding is being used for an accessory ground, which usually melts the winding.
You have already determined that the engine shuts off when the two primary leads coming out from under the mag plate are connected together, spark is killed on both cylinders. But, the crazy vacuum cut out circuit is plumbed into the stop circuit, and there are many versions of this system used. So, it is surely possible that your harness/boat wiring set up is fine, but there is a problem with vacuum cut out system wiring. So, I guess I would want to perform another test like the one you just did, but include the vacuum switch wiring in the circuit. The thing that confuses me is that just one cylinder is losing spark when the key/stop switch is turned off, so one primary circuit is finding a ground somewhere, perhaps through the vacuum cut out circuit.
Again, your harness/boat wiring might be perfectly fine, kind of hard to pass judgement on something we can not see.
Needless to say, you may have already explored these areas, I just joined this discussion and surely don't want to add confusion.