Sounds to me that when the wire is connected to the spark plug, maybe not enough voltage is being generated in order to cause a spark across the gap. When you pull the wire off of the plug, that produces an air gap for voltage to build to produce a spark. It sounds like the plug grounding strap isn't grounded for some reason. But if that were the case, then you wouldn't get a spark from the end of the wire to the tip of the spark plug, neither.
Hmm.... You changed the plug, so that rules out a plug that is broken and internally grounding itself. Is there anything in the cylinder that could ground out the spark plug electrode itself?
Does the spark plug fire if pulled from the cylinder? Is the spark gap too wide?
Try the spark tests in the dark to see if you can see sparks flying places they shouldn't be.
Heck, I know NOTHING at all about motorcycles........
Sorry...