thanks guys the plot thickens. spent hours trawling the net last night about this, the mev forum had a bit about non charging and i found two things, there is a sensor in the airbox that measures temp before the air reaches the maf sensor i hadnt plugged that in as i have no airbox, plugging that in made the charge light go out when running. but still no charge, another post mentioned a plug that lives in the boot of mx5 that needs to be plugged in, found that this is the grey/red from the alternator, i runs from the alternator up the drivers side to the boot, then plugs into the lighting loom and comes all the way back to the front to the ecu. plugging that in now gives me a small charge, battery increases by about 0.5 volts, with the car running i am getting 12.9v of it drops to 12.3 ish.
still not sure if the alternator is gubbed or the ecu is still telling it not to charge as much.
i have continuity from the alternator to the ecu on both wires but there is feeds off them doing other things not in the wiring diagrams