Ok, I will tell you all what the problem was. Pickups are directional. Whoever was monkeying around with the pickup to begin with, soldered it backwards. As soon as I talked to Ricky Stator he told me to just flip the wires, and low and be hold it worked. What is even more funny now is the wires off the pickup have no color coordination to them at all. It actually looks like the wires are crossed. Wherever that pickup came from the direction is reversed from a standard 01 cr. So now I have a complete 2001 cr ignition on the bike and an extra 2000 cdi, flywheel and the stock Honda stator coil itself. Slowride250r, it's funny that you mention the 125 coils and pickups cause I was gonna try that next if flipping the pickup wires didn't work. So now I learned that the Honda wiring schematic is wrong, a reversed pickup will cause the motor to fire 180 off, the green/white wire from the pickup goes back to ground, just because someone took the time to make the harness look like it just came out of the factory doesn't mean they knew what they were doing, and I hate when people on ebay try to sell you something they know doesn't work.
Goodnight to all,
Mike