PHeller,
On page 150 of the Haynes manual:
"On no account run the engine with the sparking plug cap(s) removed. Due to the high voltage, it is possible to damage the internal insulation of the secondary coil."
Haynes is referring to the stock TCI, so this problem is not just associated with PAMCO but is a potential problem with any high performance dual out put coil. Dual output coils do not have an internal ground reference. The secondary windings are floating but insulated from the primary winding and the core by a very thin insulating material. Under normal use, the fact that the spark plugs are grounded is incidental. The current exits the negative spark plug wire terminal, to that spark plug, through the engine head, over to the other spark plug and back to the positive spark plug wire terminal on the coil.
If you remove the wire from, say, the positive spark plug, then the path is from the negative spark plug terminal, to the spark plug, to the engine head and then to the core of the coil or through the ignition system through the thin insulation and back to the positive spark plug coil winding. We are talking about a very high voltage here, so as it jumps from the grounded core of the coil to the windings the voltage and current can burn a hole in the insulation which can become carbonized and effectively short out the coil.
Some coils, like the 17-6903 "Ultimate coil" are more forgiving of this condition because they have better quality internal insulation which basically just acts like a capacitor to allow the current to pass through non destructively.
This video also shows that if you do disconnect one spark plug, the other plug produces a very weak spark which can lead to an incorrect idle setting because the cylinder is not burning the mixture completely so when you finish with the syncing and reconnect the spark plug you may not get the results you expected.
However, the recommendation is still to not remove one spark plug wire. If you have vacuum barbs on the carb holders, then you can kill a cylinder by simply removing the hose or blind plug which has the effect of making the mixture so lean that the cylinder stops working, allowing you to set the other cylinder to the target idle speed just like you would by disconnecting a plug. In fact, the vacuum barb method is easier and more convenient allowing you to alternatively kill one and then the other cylinder to see if they are balanced.
