It sounds like your switchbox is toast.
The switchbox on this model is made up of a number of components all in one unit.
Basically it takes the AC produced by the stator, converts it to DC (for the sparkplugs to use), and stores it in one of two capacitors.
When the trigger sends a signal to the SCR switch (silicon controlled relay), the switch (tells) the respective capacitor to release energy to the coil and on to the sparkplug for it's respective cylinder.
Anyhow. To prevent the power generated from the stator from getting "sucked out" of the switchbox back to the stator itself (since it's AC, it would naturally try and travel back to its source), there are "blocking diodes" immediately after the stator connection on the switchbox (as an internal, non-replaceable component).
So, to me it sounds like the blocking diode for your high speed bobbin connection is toast. Once you disconnect the high speed wire (blk/wht) there is no where for the power to "bleed back to" and your motor runs fine (power from low speed side "stays" in the switch box capacitors until it gets the trigger signal), but when the high speed side is connected, the defective blocking diode is allowing it to travel back to the stator.
That ultimately could cause damage to your new stator (it only likes to send power out, not get it back)...