Rod, this is a friendly debate. I'm in no way taking this to be a flame or argument. I just hope we're not hijacking this thread, but I think the original poster is just going to take his car to the dealer anyway

. We may have to take this to PM if the mods think this is too off topic.
Well, to get back to things, a cylinder balance test does not tell you why a cylinder isn't producing power, only to identify which ones. Shorting the secondary spark provides a convenient method to disable the other working cylinders, thus making the one that isn't producing power stand out (due to no RPM drop when disabled).
Once you know which ones, then you will have to use other diagnostic techniques for those particular cylinders such as scope testing the secondary ignition (or primary), compression testing, and fuel injector testing. The tests you perform after cylinder balance pinpoint the reason for the misfire. I hope that answers your question about the possibility of masking a bad injector, if I understood correctly (or were you talking about the companion cylinder?).
I don't know know enough about electronics to agree or disagree with you about the effect of the spark wire's resistivity on PCM performance or electrical performance. I'm aware of the electromagnetic interference caused by low resistance wires on radio reception, however. If you can recommend me something to look at that would be great.
I disagree with you that the spark current will travel to ground when bypassing the 10kohm spark wire path with a 2 ohm ground wire. The path of the secondary spark on a waste-spark system is from one coil tower, spark plug wire to one cylinder, spark plug on same cylinder, cylinder head (block), spark plug on companion cylinder, spark plug wire on companion cylinder, and finally back to the other coil tower on same secondary winding. It's important to note that the same spark that was used to fire the first plug is used to fire the companion cylinder plug (on exhaust stroke). I have text book info to back this up in case you wanted some page scans.
With your reasoning, why wouldn't the spark go directly to ground after firing the first plug instead of jumping across the air gap of the companion cylinder plug to get to the other coil tower? It seems to me that it would be alot more difficult for the spark to jump a 0.030" air gap in the companion cylinder than it would to just go directly to ground after firing the first cylinder.
It's counterintuitive, but that's how the system works. So I don't see how shorting from one tower to the block (bypassing the spark plug and wire) will not fire the companion cylinder's plug. The path from one coil tower to the block is left intact while the companion cylinder's plug and wire is left unchanged. I can send you some scans from my engine performance book if you need more convincing.
And as far as plug wire resistance limiting surge current, you have me on that one. I really don't know much about transformers to say, or really AC electrical analysis for that matter. I'm just a stupid ME.
I don't know if I convinced you, but I know one thing for sure. I'm pooped, that was the longest post I've ever written.