First of all get a spark tester and use that for testing spark. Your method is inaccurate to say the least.
Second, if you have the coils disconnected from each other, they cant be grounding each other out. And that isnt possible in this case, since it sounds like there is an external diode pack which is on alot of Honda's. Thats what the diodes do... Kawasaki is generally the one that has problems with that since their diode is built into the coil. If the diode goes, it can cause the other coil to not fire.
Lastly, the charging system has nothing to do with spark so testing it would be pointless.