The trigger windings might need swapping around the other polarity to correct the ignition timing.
The cdi fires when it gets a signal from the trigger coil, and on older bikes(like this) it's common for the firing to be triggered by the AC voltage coming from the trigger coil rising to a certain point, then, as the revs and speed of the flywheel magnets get faster, that critical voltage needed to fire the cdi occurs earlier in the rotation, while the magnet is further from the trigger than it had fired at low revs. If the firing was too early, you might need to move the pickup coil further away from the flywheel, and/or, reverse the wires. It might be that the trigger coil is wound such that it sends the wire into a negative voltage leading up to the magnet, then a rising(positive) output after the magnet has been passed. Then you will get ignition timing that is retarded, and that gets more retarded as the revs rise.
Swap the trigger windings first, then if that doesn't get it firing at the right time, swap the capacitor charge wires about. Inside modern cdi there are integrated circuits that count the pulses of AC coming from the stator, and only fire after a certain number of AC waves and then a trigger signal.
To be sure whether the cdi is going to run the bike(and it probably will), then you need to try the wires in all four possible combinations of connection polarity.