I did some research and can answer my own question. A CDI multiplies the spark by a minimum of 10 fold. As such the input spark I am receiving at 50v should be coming out of the CDI at at least 500v, therefore I have a bodgie CDI.
The research I did also tells me the ohms I am reading across the coil is about right too, again must be bodgie CDI.
If Luke of Leigh are reading can you confirm what volts I should be reading from the PE400 stator? I have read quite a few good articles on rewinding a stator yourself and it doesn’t sound to hard so if my volts are down I may have a crack at that also.