Well, my GY6 ignition coils arrived today, and although I was a little unsure if a standard GY6 CDI unit was able to drive 2 ignition coils, I was happily surprised when I saw nice strong spark at both plugs! A bit of assembly work later, I have a running quad. Multiple problems made this ignition system hard to troubleshoot, but here's what I found;
-loose connections in 2 pole plug from pulse generator. I ordered new connectors off ebay, cheap from Taiwan.
-bad CDI. I took a chance and ordered a few GY6 type CDI's off ebay, $4 each, shipped from China(thus answering the question can you parallel 2 coils off a standard GY6 CDI - YES!!)
-one bad ignition coil. Once again, went with the GY6 type, $14 for the pair shipped from China
-bad connections on CDI 2 and 4 pin connectors. It appears the spade (female) part of these connectors have spread, so even though the plug is inserted firmly, there is no connection from the wiring harness to the CDI pins. Once again, to ebay, $12 from Taiwan.
So, for less than $50, I have all new connections and everything north of the stator is new. Thanks LynnEdwards for your time and advice, I have a far greater understanding of CDI ignition systems now, and I honestly believe I could tackle any problems this ignition system might throw at me in the future.
I hope this thread can help point someone else in the right direction, I've noticed alot of headers saying HELP NO SPARK!.
Happy Holidays everyone, heading out to do some serious quadding!!!

 

I'm glad things ae working out for you .

But after thinking about this a lot I have some concerns that may or may not be valid.

Right now everything is working, and the output of the CDI is split evenly across two ignition coils, with half the spark energy deliviered to each spark plug. But suppose one plug (the left one let's say) gets fouled a bit, and that requires more voltage to jump the plug gap. That higher arc voltage may shift the CDI output power more to the unfouled lower voltage right spark plug, leaving less power for the left fouled plug causing it to foul up some more. And off we go in a regenerative loop... Then you end up with only one plug working.

That's my concern... Perhaps it is unfounded. I don't really know that a fouled plug takes more voltage to fire. If it took less voltage then it would steal more power from the CDI which would clear the plug and instead of feeding back regeneratively making the problem worse. Instead it would be self healing.

Time will tell. You could always mitigate this with two GY6 CDIs feeding two ignition coils off one trigger signal....

I hope all goes well with this pioneering project. Thanks for reporting back, and please report back if you run into prblems later...