125-200cc 07 WR 125 Ignition

I need some help diagnosing a faulty ignition.
The bike never really revved out fully. It always seemed to be held back at the top end, but ran ok everywhere else.
I put a light on it and found out that it was firing twice, about 180 degrees apart.
Now, I've since replaced it with a PVL and the bike really rips now, all the way to the top so I know something was wrong.
Any ideas on what went wrong? I would like to fix it and keep it as a spare.
Thanks, JC

Hmm, you swapped complete setups with the PVL?

Yes, the whole system. I also added an 8 oz flywheel weight to it.
My son said that it was like a whole other bike. It rips now.
He finished 12th Overall out of 131 last weekend.

Any ideas on what went wrong with the factory set up?

I think this is the result of an analog ignition, just a simple system. I was doing some reading and it appears a lot of traditional analog systems will fire twice, once on compression and once on exhaust(180 deg apart as you mentioned). A digital ignition timing is more detailed and only fires once per rev. As for it not running clean on top, I believe some people that had this issue needed to make sure they used a resistor type plug. But I know you've been on these 125s awhile and probably had heard of that. Not sure what else would cause that?? As far as I'm concerned the CR type(digital ignitions) are way better performance wise and easier to replace. Most any MX 125 has the same kokusan parts.