So, the new flywheel didn't fix it, nor did another flywheel off of another newer quad. Just for fun I ordered a cheap CDI unit from Amazon and bang! Spark again. I can still put the original CDI on the other bike and it runs. I suspect a tolerance stack issue, weak pickup/flywheel matched with a weak CDI. The other bike must have a slightly stronger pickup and/or flywheel so the CDI works with it. Anyway, now that that works I need to find the source of an engine knock.
thanks